When I create a Bloodrager5, Dragon Disciple 2 character, PCGen is calculating my bloodline to be 8 levels instead of 7, but when I am just a Bloodrager7 it is working properly. I thing something is still not being calulcated right between the DD Bloodline and Bloodrager Bloodline.
Primary Example is the Breath Weapon. You can that and 8th level bloodline, but a my level 7 Bloodrager5,DD2 had gained it for some reason (as well as the damage increase on his claw attack)
Looking into this a little, I think the Dragon Disciple class is a repeated section on line 1885:
BONUS:VAR|BloodlineLVL|DragonDiscipleLVL BONUS:VAR|BloodlineLVL|classlevel("Dragon Disciple")
If I remove that second section, the classes are stacking the way they should be.
Please grab 6.05.06 and confirm this is fixed for you.