I noticed a (most likely) related issue back in build 31. Here's the post I made in the thread for that release:
I was just trying to split and convert an album ripped into a single APE file via the associated cue sheet when I noticed that the last track isn't split correctly. Media Center ends up encoding the whole album and calling it the final track. I was converting to Musepack, and tried both "Leave original file; add destination file to library" and "Replace original file on disk and in library" modes with no success; the same thing occurs regardless of the mode I choose. I set MC to covert 4 files at the same time (quad core processor), if that matters. This functionality has worked for me before (recently purchased and upgraded to MC15 from MC13), so I think this is a bug.
I'd really like to have this issue resolved, because this is a feature I use quite often!
Thanks,
-Lenny