I know there are limits on how much/often you can spend your favor points to speed up skill learning, but I'm pretty sure it's also bugged -- I was in the midst of donating a bunch of things to one of the giants, when I switched to another skill to verify that that skill's time couldn't be brought down any more, then switched back to the original skill -- and all of a sudden I couldn't spend the favor points on that skill anymore, either, when I clearly saw that I would've been able to before. Very frustrating because I feel like I just wasted a bunch of good items.
If this isn't a bug, then I think we definitely need more clarifications on all of the factors limiting when favor points can be spent, because I thought I knew the 'rules' but apparently I don't.