I had this problem with music players under Linux that cuts off the last few secs on AAC files that was encodeded by the old Feb 07 version of Nero AAC, due to a bug that writes a incorrect time length on the MP4 container. Which i managed to fix with mp4box.
You could try mp4box with the -ipod format switch on a few albums, and see if it fixes your problem.
My old MP4 to M4A script, which requires MP4box.exe:
CODE
FOR /R %1 %%I IN (*.mp4) DO MP4Box.exe -ipod "%%I"
FOR /R %1 %%I IN (*.mp4) DO REN "%%I" "*.m4a"
But am sure that the Zune wouldn't be affected by that issue.