When you give a Human Rogue (and I'm imagining the same happens for Ninjas and other races that give out the same FCB) and you pick 1/6 of a Rogue Talent for favored class bonus, you get empty boxes on your character sheet.
I imagine the type of the bonus is being marked as a displayable special quality, while it should be hidden.
Attach a pcg, I don't know which "Bonus Rogue Talent" (of which there are 5 or 6) is causing your issue. (Funny though, only one is set up to kinda work...)
I'm not seeing any boxes, loaded Core Supplements (Which includes the ARG). Added x2 of the FCB for a Human Rogue. Level 6.
Please verify where exactly this was happening. PDF, clear. Preview, clear.
Sure, adding it to the main post... it is not a PDF issue though, it's a character sheet preview issue.
Completed: At revision: 24897