Clip Splitting dropping audio in Quicktime

I work in the film industry and often have to put together demo reels and promotions clips from TV shows, etc. My normal workflow has me opening up episodes in Quicktime, quickly scanning an episode and using the clip splitting function to create a much smaller reference file for use in FCPX in order to keep the editing process quicker and library files smaller.

However, Quicktime is dropping audio randomly when I use this function now during the editing process. I'll remove a clip and it'll just stop playing audio, and then start again when I clip again. If I ignore the audio drop and save the file, those audio drops are saved to the new files. The original files obviously do not have an audio drop.

My current workout around is to do the editing in iMovie, but that leads to much larger reference files, (larger than the originals in most cases!), and scanning in iMovie is much much slower than in QuickTime.

Anyone else have this issue? Any solutions?