The abilities sometimes get shuffled around when you upgrade their skills (or at least, they did during beta ..).
If you press the little deck of cards icon near your skill bar and choose the 3rd option, you'll see all three levels of skill bar. The top one should be your alt-keys. Find where your BO abilities have been stuck, and move them into the slots you want them with (right-click and drag). If they're not there at all, bring up your power list ('P') and move them from there.
This is from memory (I'm at work), so the details might be a little off.