There is a way to fix it in your tunebite folder open up the config.ini and play around with the settings for volume low/high and timeout thresholds, I got mine down to only 2 seconds over the actually song length.
Or if you just convert to ogg instead of mp3 then convert ogg to mp3 using a different programit offers 100% perfect length.
Exactly which settings did you change and what did you change them to?
How do you uaw musicstacker? Is asking for License Acquistion. Need to import song into library, trying to the songs do not show up.