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Audio sync points - is there such a thing?

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Here's my problem. I'm starting a project where I want to sync an audio stream from a.avi (mp3 or ac3) to a video file, b.mkv for that matter. the video content is identical (credits aside)
a.avi is 25FPS
b.mkv is 23.976FPS

This is what is giving me the best result yet:
I'm converting a.avi to a.mp3 with 23.976 frames using meGUI. (I suspect that meGUI isn't giving me perfect results but I'm not sure)
Then I'm using MKVMerge to mux those two and maybe giving it a bit of delay as needed. The problem is that it's not perfect. I don't know what causing it but even if the sync is 100% accurate at the beginning of the movie, somewhere along the middle the audio will be half a second - 1 second out of sync.
I know that with subtitles you can set syncing points, is there something like that for audio?
Can you think of anything else that might help me out?

Thanks

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