Merge multiple audio tracks from different files into 1 video file - sync

[heinza]

Hi guys,
I am having trouble making a single video file with multiple audio tracks.
I have a movie with better visual quality that I want to use for the video part, and the same movie in a lower video quality file, from which, though, I need to extract the audio in a language that is not present in the first one.
I'm on a Mac using Lion OSX and have tried with MKVToolInix with no luck.
What's strange is that, according to MediaInfo, both files have the same fps rate and nearly identical running time, and the merged-in audio is nearly in sync at the start of the movie in the new file, but gets out of sync later on...
Another movie I've got, however, needs to be re-synced as well, as the 2 files don't match 100% in the first place, plus the fps rate is different (29 vs. 25).. Again, with MKVToolInix, I managed to set an offset time for the added audio track, but it gets out of sync later into the movie as the fps rates don't match, and I have no idea how to change the fps rate for an audio file.. (no option in MKVToolInix, only for video).
What tools can I use, possibly on a Mac, to merge and sync files and solve these problems?
Thanks!

[teodz1984]

Just rip everything back from the original DVD /BR source.... choose the language you want from the DVD.
Very hard to sync from different rips...

[heinza]

Unfortunately that's not an option for me because they come from two different sources..
All I have to work with are the two movie files to be merged into one..