I know exactly what's happening now. Yes, it's due to short tracks not being handled gracefully. PCMBUF sees an auto skip (end of playlist is always auto skip), and the file is short enough that the crossfade is still active at the time, so it bails out (apps/pcmbuf.c line 703). It's not specifically end-of-playlist; having three files in the directory after the two provided will cause a bail on the second and transition to the third.
So, I got this one and have a couple more bugs in the heap that need to be handled. I've been derelict lately.