A quick search on http://geck.gamesas.com/index.php/MatchRace yields a few threads. http://www.gamesas.com/index.php?/topic/1051242-bad-matchrace/ seems to describe a situation where M3hdi tried to change the player race into a custom race with custom textures. While no solution is given, one could try to esmify the mod with the races? Uglulyx had a similar problem in http://www.gamesas.com/index.php?/topic/1072801-trying-to-change-the-players-race-using-matchrace/ and there are a number of interesting points and ideas. One interesting idea is to ensure that there are child (and possibly old and oldaged) versions of the custom races. You may also find http://www.gamesas.com/index.php?/topic/1106990-duplicating-the-player/ interesting.
It should also be noted that the only Fallout3.esm usage of MatchRace is to match the race of James ("daddy") to the race selected by the player, using these lines
; dad matches player's race and face MQDadREF.MatchRace player ; match face MQDadREF.MatchFaceGeometry player CGMatchFace