It seems, that you are stumbled over a known problem situation when applying the MP3Gain utility in default mode writing APE tag.
Check the Mp3tag settings for "Mpeg" and understand the priority how different tag types will be used within Mp3tag.
Use mp3gain.exe to be compatible with the ID3 tagging system.
Better use foobar2000 to write non destructive ReplayGain values into ID3 tag fields.
Find informations there ...
Anzeigeformat in Spalte "Tag" (revisited)
.. and there ....
http://www.google.de/search?&q=site:community.mp3tag.de+APE+OR+mp3gain+OR+"tag+priority"
DD.20110629.0724.CEST