Smplayer incorrectly works after jumping to a specific time while watching a mkv video

Does this still happen if you turn off the "correct pts" option in Preferences -> Advanced?

Yep. No difference.

I tried some mkv files and I can't reproduce this problem.

It would be helpful if you could give some info about your configuration, like the video and audio drivers you're using in smplayer, or the mplayer log after the problem happened.

Amongst others:
driver\vo=xv
driver\ao=alsa

If this matters:

$ lspci | grep VGA
00:02.0 VGA compatible controller: Intel Corporation Mobile 4 Series Chipset Integrated Graphics Controller (rev 07)

Could this issue cause another one - inappropriate delay of subtitles? (I have to move them once in a while, finally even by 30 seconds - subtitles are OK as I have the same video in avi format and there it works just fine).

It seems the bug is gone if I choose OSS audio driver instead of ALSA in smplayer settings. Why would it work?

Worth noting may be that I do *not* use PulseAudio - it was too buggy for me so now I rely on a pure ALSA itself.

Hmm... The same problem occurs when I use VLC (I have to check if the problem persist after a reboot). However, Totem works fine.

VLC output (maybe this is another error, I don't know...):
On first try:

$ vlc GCBC_SCR.XviD.avi
VLC media player 1.0.2 Goldeneye
[0x1be4998] main libvlc: Running vlc with the default interface. Use 'cvlc' to use vlc without interface.
QPainter::begin: Paint device returned engine == 0, type: 1
QPainter::begin: Paint device returned engine == 0, type: 1
[????????] x11 video output error: X11 request 132.19 failed with error code 8:
 BadMatch (invalid parameter attributes)
X Error of failed request: BadMatch (invalid parameter attributes)
  Major opcode of failed request: 132 (XVideo)
  Minor opcode of failed request: 19 ()
  Serial number of failed request: 107
  Current serial number in output stream: 108
// here it failed

On the second try:

$ vlc GCBC_SCR.XviD.avi
VLC media player 1.0.2 Goldeneye
[0x174c998] main libvlc: Running vlc with the default interface. Use 'cvlc' to use vlc without interface.
QPainter::begin: Paint device returned engine == 0, type: 1
QPainter::begin: Paint device returned engine == 0, type: 1
X Error: BadMatch (invalid parameter attributes) 8
  Extension: 132 (Uknown extension)
  Minor opcode: 19 (Unknown request)
  Resource id: 0x6c00005
X Error: BadMatch (invalid parameter attributes) 8
  Extension: 132 (Uknown extension)
  Minor opcode: 19 (Unknown request)
  Resource id: 0x6c00005
X Error: BadMatch (invalid parameter attributes) 8
  Extension: 132 (Uknown extension)
  Minor opcode: 19 (Unknown request)
  Resource id: 0x6c00005
// into infinity...

Ah. Sorry, I posted it on the wrong bug report.