MakeitOne does not alter your tracks, if you experience noise/glitches/hiccups between packed tracks it is down to the MP3 decoder that is being used and how it processes the header information at the begining of each track. It is likely that any MP3 tags attached to each track can increase the problem.
If you wish to minimize the problem it is recommended to remove all MP3 tags (using something like: http://sourceforge.net/projects/massid3lib/ ) before packing.