Matroska chapters timecode alignment

[SamLowry]

I'm trying to concatenate several video clips and define chapters that refer to the beginning of each clip.
The problem is that I can't get the precision I need. I want the chapters to be defined with a video frame precision, so, when I navigate to next chapter the player will start playing from the first video frame of the next part.
I know timecodes can be defined with nanoseconds precision, but this doesn't seem to help because there are quite a few factors that limit the possible timecodes for chapter navigation i.e. cluster timecodes, cues definitions, lacing etc.
Is it possible to use mkvinfo's output to get the proper values that chapter timecodes should be aligned to?

The ideal solution would be a tool that I can navigate frame by frame (like virtualdub) and mark specific frame as chapter start. Is there such a tool?

[thewebchat]

Edit: Oh, oops, did not read your question correctly. If you need exact frame times, just navigate in VirtualDub and copy the timestamp it shows in the bottom. You can only jump to keyframes reliably with Haali's splitter but since you're concatenating clips that should be no problem.

[SamLowry]

I have tried to do the job with mkvmerge and with avi-mux gui. Avi-mux even has automatic chapter generation based on clips being concatenated.
When I play the resulting mkv and try to navigate chapters, the player seeks to positions that are between 1 second before and 1 second after the first frame of that part, which is not acceptable for me. The players I have checked are VLC, XBMC and PopcornHour. VLC's and XBMC's mkv demuxers are based on libavformat. Is it possible this issue to be related to libavformat?

Please, advice!