Apparently we are not alone in seeing several lopsided home run calls. 

http://www.philly.com/dailynews/sports/20090529_Paul_Hagen__Mets__latest_replay_home_run_anything_but_conclusive.html

This Philadelphia Journalist notes that of the 12 reviewed home run calls in baseball 5 have been during met's games, and all 5 were reviewed in favor of the mets.  This can't be anywhere near normal since homers can only be overturned if they are conclusive.  conclusive is a very high standard legally.