PCGen, as far as I understand, does not allow to remove or replace automated feats and abilities while there are some feats with "replaces [race]'s racial feat [feat]" in rule texts.
E.g. Half-elf has "Multitalented" racial feat that would allow them to get bonuses from leveling any of two classes up, but if a player would never take any class other than his starting, this feat becomes useless, and it's natural for him to trade it for another available racial feat,
UPD: appears that i had corrupt version of the program. re-installed, works fine