For some live sets I have, I am partial to a single file/track for the entire set/album. Unfortunately some of the sets have been divided by tracks into single files.

I have been using the wonderful utility MusicCutter to join the files as one. I like to check the quality after doing so, so I load up the newly created single file and listen to each of the join points (as indicated by my cue sheet).

I notice that some tracks will join without a single gap for the entire set, while others will have a variable length gap per each track--sometimes barely audible and other times distractingly noticiable (and either way wholely unacceptable). Unfortunately, since these are live recordings, I rarely have access to the original file in a complete and preferrably lossless form (yes I am aware of communities like etree). I have also ensured that ID3v2 tags are removed.

Do the gaps appear because the individual tracks do not observe proper frames lengths? If so, is there a join-utility that will ignore the frame length and construct the file without padding the tracks to fit within a frame? ...or is this related to the codec used in the initial MP3 files?