I've imported some .MTS clips into a Premiere Pro CC 2015 project and I'm noticing the audio jumps around consistently (Both in the sequences and in the project windows). I've tried encoding the file to H.264 in Media Encoder but the issue seems to "bake-in" to the file in that process. The raw, uncoded MTS file on the hard drive plays perfectly fine in VLC. Is this a project issue? And how can I solve this? Thanks.
Word to the wise, never convert something to H.264 to edit. H.264 is not an editing codec, it's a watching codec. Premiere claims to be able to handle it, but only if you want to pull your hair out.
You want to convert to ProRes 422 if you're on a Mac. What do you mean by jumps around? Try using ProRes and Match Settings and see if that helps. Did you look at the Audio Gain and Channel settings? Maybe one channel is screwed up? Good luck!