Sorry to dig up an old post, but there were no replies, and this is the exact (almost) problem I just had. I've used audactity a bunch without issues, but in my last mastering project I got 2-3 second blank spots at the end of each track that is traced back to audacity.
24/48 master file loaded into audacity (1.3.2 i think). exported to 16 bit and resampled to 44.1. i did track split (selected cursor to end, hit split, split looked fine). then when i exported the tracks, 2 seconds of silence was added to each track. very bummed as i upped the files based on my prior experience without this issue. should have done additional QC, but i've never encountered this before.
FWIW - i edited the .wav file slightly, then exported it as one file, and split it in cd wave. that worked fine. very bizarre.