I've sent in a report from the app, and I've been able to narrow down the issue to purely writing on the external SD Card. Everything syncs perfectly onto internal device storage. But when I sync onto the external SD card, files are incomplete, saved as .bts files, and the transfer is unstable. I think this may be related to MM 6.0 storage changes. My permissions for the SD card are correctly setup, as other apps have no issue with this.
I've seen plenty of users on XDA and other forums with this same issue description, hopefully you guys can get this worked out.