Some files are being left as mkvs...not converting to mp4

You can read about the conversion process here:

Attach your mcebuddy.log file and I can tell you what you’ve configured. Basically MCEBuddy will monitor what you asked it to monitor and then convert it to whatever you asked it to convert to. If you asked the output as MP4 it’ll create MP4 and not MKV’s. It won’t create anything you haven’t asked it to do.

If it’s listing the MKV’s on scanning then that’s probably what you’ve asked it to monitor.