Innovation FIRST sent me an example of the bad part. A recommendation was made on the ifirobotics.com forum in this post:
http://www.ifirobotics.com/forum/viewtopic.php?t=174
A pdf file with a picture showing a bad gear mated on the shaft is referenced in the above post link. I am also updating the transmission manual page 2-9 to show which direction to put the gear.
Referencing page 2-9, the FRC-2005-112-005 and -003 should be oriented as shown in the picture. The gear and the shaft are not symmetric. If you place the gear on from the same side as the bearing (not as shown), then you can use a brass or dead blow hammer to get the faulty gear on the shaft. This should cause no pre-mature wear on the gear and it should function normally. The gear does not have to be re-worked.
-Paul