Subtitling HD video

Good morning geeks, I'm running XP Home SP3.
I do a little video subtitling and have run into a problem I think I know what it is but not how to solve it. I want to take a subtitle .srt created for a 700MB .avi file and re-time it so that it works with an HD video in a .mkv container. I normally use Visual SubSync, but for this have also tried DivX Media Subtitler and Subtitle Workshop, and none do the job.
I can identify where the subtitle needs to be using a .wav form or time counter, but when I enter the subtitle, or a new time for an existing subtitle, then playback it is way off.
I think the issue is that for a 700MB .avi file the audio track is 2 channel, but with an HD video the audio track is usually 5.1 channel. The programs I use must not be capable of managing the added complexity of syncing with the 5.1 audio track.
So, what to do...?

Thanks

 

I realise this is not a direct answer to your question, but it may be helpful...

I believe that in VLC media player, you can add sub's and adjust the timing on the fly to make it right.

I've never tried it myself, but VLC is an amazing tool if you can work it proeprly (it does a hell of a lot more than just play ANY video format )