Media Encoder 2018 Audio cuts out on in mid clip when converting MTS to ProRes422

Hey, working on a big project (for me anyways) with tons of files spread across almost 2 dozen bins. Decided to use Media Encoder to convert/uncompress MTS files and import them as ProRes mov files. Having several issues, including out of sync audio, audio cutting out in mid-clip. Not for all clips, but enough to make me trash all the mov files I just converted and go back to import the original MTS files. What is going on? Never had any issues at all until I upgraded to Adobe CC 2018. Thinking you guys dropped the ball on this release. The reason I decided to convert the MTS files in the first place was that on import Adobe Premiere would randomly assign audio to a clip from a whole different set of clips shot on different days and placed in different folders. Again, what in the world is going on? These are major issues that shouldn't be happening at all.