I just found this program after having searched a lot and also tinkering with my own similar program.
I've really gone through a lot trying to find a solution that fits my needs so I was really excited finding this one that seems to do just what I want and is really user friendly as well.
I haven't purchased yet but will definitely do so if my problem gets solved.
The problem I'm having is that for the majority of my video collection that I need to perform cutting for, the audio is not present in the output-file.
So far all of these files have AAC codec.
I viewed the output-audio in an audio-editor and it looked like a 3 second clip, with first 2 seconds being silence, and the third just scrambled noise.
The problem is only present in High-speed mode and not when re encoding.
I uploaded a sample clip to my google drive here. Hoping this can be solved somehow.