When choosing a bloodline for sorcerer and leveling up to the point where you receive bonus spells they count against your known spells. (in screenshot I have arcana bloodline, so identify and invisibility shouldn't count as known spells when trying to learn spells (level 5))
windows 7, java 7
This appears to be fixed in the latest version of PCGen. (6.01.4 or when the next release of 6.0 comes out).