mii-tool reporting incorrect duplex mode

Status changed to 'Confirmed' because the bug affects multiple users.

Just a stab in the dark here, but could this be as simple as the fact that 1000baseT-HD is listed before 1000baseT-FD in the capabilities? I noticed the FD comes before HD for 100 and 10.

eth0: negotiated 1000baseT-HD flow-control, link ok
  product info: vendor 00:07:32, model 17 rev 2
  basic mode: autonegotiation enabled
  basic status: autonegotiation complete, link ok
  capabilities: 1000baseT-HD 1000baseT-FD 100baseTx-FD 100baseTx-HD 10baseT-FD 10baseT-HD
  advertising: 1000baseT-HD 1000baseT-FD 100baseTx-FD 100baseTx-HD 10baseT-FD 10baseT-HD flow-control
  link partner: 1000baseT-HD 1000baseT-FD 100baseTx-FD 100baseTx-HD 10baseT-FD 10baseT-HD flow-control

Oh, and ethtool output for what it's worth:

Settings for eth0:
 Supported ports: [ TP MII ]
 Supported link modes: 10baseT/Half 10baseT/Full
                         100baseT/Half 100baseT/Full
                         1000baseT/Half 1000baseT/Full
 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)
 Link detected: yes

the bug is still present in 14.04.1 LTS:

[root->~]# mii-tool eth0
eth0: negotiated 1000baseT-HD flow-control, link ok
[root->~]# ethtool eth0
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
 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

Still present in 15.10; I rewired a new jack twice before I realized what was going on here.

# lspci
00:00.0 Host bridge: Intel Corporation 4th Gen Core Processor DRAM Controller (rev 06)
00:02.0 VGA compatible controller: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics Controller (rev 06)
00:03.0 Audio device: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor HD Audio Controller (rev 06)
00:14.0 USB controller: Intel Corporation 9 Series Chipset Family USB xHCI Controller
00:16.0 Communication controller: Intel Corporation 9 Series Chipset Family ME Interface #1
00:1a.0 USB controller: Intel Corporation 9 Series Chipset Family USB EHCI Controller #2
00:1b.0 Audio device: Intel Corporation 9 Series Chipset Family HD Audio Controller
00:1c.0 PCI bridge: Intel Corporation 9 Series Chipset Family PCI Express Root Port 1 (rev d0)
00:1c.2 PCI bridge: Intel Corporation 9 Series Chipset Family PCI Express Root Port 3 (rev d0)
00:1c.3 PCI bridge: Intel Corporation 9 Series Chipset Family PCI Express Root Port 4 (rev d0)
00:1c.4 PCI bridge: Intel Corporation 9 Series Chipset Family PCI Express Root Port 5 (rev d0)
00:1d.0 USB controller: Intel Corporation 9 Series Chipset Family USB EHCI Controller #1
00:1f.0 ISA bridge: Intel Corporation 9 Series Chipset Family H97 Controller
00:1f.2 SATA controller: Intel Corporation 9 Series Chipset Family SATA Controller [AHCI Mode]
00:1f.3 SMBus: Intel Corporation 9 Series Chipset Family SMBus Controller
02:00.0 Ethernet controller: Realtek Semiconductor Co., Ltd. RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller (rev 06)
03:00.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev 41)
05:00.0 Ethernet controller: Intel Corporation 82574L Gigabit Network Connection

PCI ID of Controller is the one integrated into my Gigabyte H97M-D3H motherboard.

02:00.0 0200: 10ec:8168 (rev 06)

# mii-tool
SIOCGMIIREG on eth0 failed: Input/output error
SIOCGMIIREG on eth0 failed: Input/output error
eth0: negotiated 100baseTx-FD flow-control, link ok
eth1: negotiated 1000baseT-HD flow-control, link ok

# ethtool eth1
Settings for eth1:
 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