I have ripped a few clips and would like to compile them into 1 clip.
Ripped ? from a DVD ? you have VOB files ?

When I use tmpgenc to compile the clips the audio gets off track.
compile ? Convert ? from what to what ?

You need to explain more what you are doing !

If you have "captured" or have .mpg files, you can join them all with TMPGEnc Merge&Cut

But if they are not correct (Authoring and burning) you need to use TMPGEnc to convert them.