MeGUI sporadically doesn't encode full DTS track to AC3

I'm working with some DTS audio, converting it to AC3 within an MKV container via MeGUI without touching the video, and I'm having unique issue. Every couple of files, I'll hit a random dud where it will encode about 80% of the DTS track to AC3, and then the rest will be silence. Seemingly happens at random. Choosing different decoders and settings doesn't alleviate the issue.

Any ideas?