OK, I think I have found the reason for this bug. It is not due to stage 2 in power nap, but rather stage 1 - during powersave mode the ethernet configuration for the card is changed, which deactivates wake-on-lan.

Since power nap first enters in stage1 then stage2, when the computer is turned off (or suspended) in stage 2, the wake-on-lan is deactivated... Of course I do *not* see this when manually shutting down, because my typing on the console or through ssh gets the computer out of powersave mode.

Here is the log file which demonstrates this. It is produced by a while loop which logs the end of /var/log/powernap.log and the result of "ethtool eth0" every 5 seconds. As you can see below the first two logged entries (at t=0s and t=5s) have "Wake-on: g" but at t=+10s there is "Wake-on: d" which I assume means deactivated...

=> I am not sure where power nap changes this, isn't it supposed to just change speed ?

####### Time series of /var/log/powernap.log and "ethtool eth0"  at 5s intervals #########

samedi 28 avril 2012, 11:24:08 (UTC+0200)
2012-04-28_11:23:45 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [3] seconds
2012-04-28_11:23:46 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [2] seconds
2012-04-28_11:23:46 WARNING  Taking action [/usr/sbin/powernap]
2012-04-28_11:23:50 WARNING  Taking recover action [/usr/sbin/pm-powersave false]
2012-04-28_11:23:59 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:00 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:02 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:05 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:06 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:08 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
Settings for eth0:
	Supported ports: [ TP MII ]
	Supported link modes:   10baseT/Half 10baseT/Full 
	                        100baseT/Half 100baseT/Full 
	                        1000baseT/Half 1000baseT/Full 
	Supported pause frame use: No
	Supports auto-negotiation: Yes
	Advertised link modes:  10baseT/Half 10baseT/Full 
	                        100baseT/Half 100baseT/Full 
	                        1000baseT/Half 1000baseT/Full 
	Advertised pause frame use: Symmetric Receive-only
	Advertised auto-negotiation: Yes
	Link partner advertised link modes:  10baseT/Half 10baseT/Full 
	                                     100baseT/Half 100baseT/Full 
	                                     1000baseT/Half 1000baseT/Full 
	Link partner advertised pause frame use: Symmetric Receive-only
	Link partner advertised auto-negotiation: Yes
	Speed: 1000Mb/s
	Duplex: Full
	Port: MII
	PHYAD: 0
	Transceiver: internal
	Auto-negotiation: on
	Supports Wake-on: pumbg
	Wake-on: g
	Current message level: 0x00000033 (51)
			       drv probe ifdown ifup
	Link detected: yes


samedi 28 avril 2012, 11:24:13 (UTC+0200)
2012-04-28_11:23:50 WARNING  Taking recover action [/usr/sbin/pm-powersave false]
2012-04-28_11:23:59 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:00 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:02 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:05 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:06 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:08 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:10 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:11 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:12 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
Settings for eth0:
	Supported ports: [ TP MII ]
	Supported link modes:   10baseT/Half 10baseT/Full 
	                        100baseT/Half 100baseT/Full 
	                        1000baseT/Half 1000baseT/Full 
	Supported pause frame use: No
	Supports auto-negotiation: Yes
	Advertised link modes:  10baseT/Half 10baseT/Full 
	                        100baseT/Half 100baseT/Full 
	                        1000baseT/Half 1000baseT/Full 
	Advertised pause frame use: Symmetric Receive-only
	Advertised auto-negotiation: Yes
	Link partner advertised link modes:  10baseT/Half 10baseT/Full 
	                                     100baseT/Half 100baseT/Full 
	                                     1000baseT/Half 1000baseT/Full 
	Link partner advertised pause frame use: Symmetric Receive-only
	Link partner advertised auto-negotiation: Yes
	Speed: 1000Mb/s
	Duplex: Full
	Port: MII
	PHYAD: 0
	Transceiver: internal
	Auto-negotiation: on
	Supports Wake-on: pumbg
	Wake-on: g
	Current message level: 0x00000033 (51)
			       drv probe ifdown ifup
	Link detected: yes


samedi 28 avril 2012, 11:24:18 (UTC+0200)
2012-04-28_11:24:02 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:05 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:06 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:08 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:10 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:11 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:12 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:13 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [3] seconds
2012-04-28_11:24:15 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [2] seconds
2012-04-28_11:24:15 WARNING  Taking action [/usr/sbin/powernap]
Settings for eth0:
	Supported ports: [ TP MII ]
	Supported link modes:   10baseT/Half 10baseT/Full 
	                        100baseT/Half 100baseT/Full 
	                        1000baseT/Half 1000baseT/Full 
	Supported pause frame use: No
	Supports auto-negotiation: Yes
	Advertised link modes:  10baseT/Half 10baseT/Full 
	                        100baseT/Half 100baseT/Full 
	                        1000baseT/Half 1000baseT/Full 
	Advertised pause frame use: Symmetric Receive-only
	Advertised auto-negotiation: Yes
	Link partner advertised link modes:  10baseT/Half 10baseT/Full 
	                                     100baseT/Half 100baseT/Full 
	                                     1000baseT/Half 1000baseT/Full 
	Link partner advertised pause frame use: Symmetric Receive-only
	Link partner advertised auto-negotiation: Yes
	Speed: 1000Mb/s
	Duplex: Full
	Port: MII
	PHYAD: 0
	Transceiver: internal
	Auto-negotiation: on
	Supports Wake-on: pumbg
	Wake-on: d
	Current message level: 0x00000033 (51)
			       drv probe ifdown ifup
	Link detected: yes


samedi 28 avril 2012, 11:24:23 (UTC+0200)
2012-04-28_11:24:02 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:05 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:06 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:08 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:10 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:11 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:12 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:13 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [3] seconds
2012-04-28_11:24:15 WARNING  Entered into GRACE PERIOD. Action [/usr/sbin/powernap] will be taken in [2] seconds
2012-04-28_11:24:15 WARNING  Taking action [/usr/sbin/powernap]
Settings for eth0:
	Supported ports: [ TP MII ]
	Supported link modes:   10baseT/Half 10baseT/Full 
	                        100baseT/Half 100baseT/Full 
	                        1000baseT/Half 1000baseT/Full 
	Supported pause frame use: No
	Supports auto-negotiation: Yes
	Advertised link modes:  10baseT/Half 10baseT/Full 
	                        100baseT/Half 100baseT/Full 
	                        1000baseT/Half 1000baseT/Full 
	Advertised pause frame use: Symmetric Receive-only
	Advertised auto-negotiation: Yes
	Link partner advertised link modes:  10baseT/Half 10baseT/Full 
	                                     100baseT/Half 100baseT/Full 
	                                     1000baseT/Half 1000baseT/Full 
	Link partner advertised pause frame use: Symmetric Receive-only
	Link partner advertised auto-negotiation: Yes
	Speed: 1000Mb/s
	Duplex: Full
	Port: MII
	PHYAD: 0
	Transceiver: internal
	Auto-negotiation: on
	Supports Wake-on: pumbg
	Wake-on: d
	Current message level: 0x00000033 (51)
			       drv probe ifdown ifup
	Link detected: yes