I have encountered this also. I think the problem stems from the fact that the Waypoints put you into 'Ground Targeting Mode' which is used for skills like Flaming Arrow and Shadow Flare, among others. So it's use is prevented while casting all spells to prevent a conflict of multiple ground targeting modes being used simultaneously. I don't know how the system works, but it sounds like a half decent theory at least. Anyone know if casters can initiate their Limit Break when in mid-spell cast?