Raising this thread from the dead!
So I found what I consider "the best" solution (so far) to fixing the gaps at the beginning or end of audio loops.
I recently tried out the digital audio workstation (DAW) REAPER. It's pretty sweet and made by the dude who made Winamp. First 60 days are free (all features available) and after that you would have to pay for a license. The cost is $60 which is totally worth it. Most DAW's of this caliber run $100+ easily.
Anyways on to the fix. Upon trimming your audio and prepping it to be a loop, you would go to File>Render. When the render box pops up, you'll see under "Time Bound" a check box for "Tail". Uncheck that. It'll prevent the codec you use (mp3, wav, aiff, etc) from adding that annoying empty gap to the end of the export.
If you find yourself having blank audio at the beginning AND end, check out the REAPER manual here and refer to section 21.5 "Rendering a finished song": it explains how to lay down markers and tell the DAW to export ONLY what is between those markers. Pretty handy.