This could be intentional but feels like a bug. Each time flawless advance is used the duration is refreshed. If Flawless advance is used near the tail end of the duration however, it casts appropriately, but does not refresh the duration.
Here to say I've got this issue too. I think it has something to do with it being CAST during the recast window, but because of the charge, the actual attack/spell going off after the recast window is already finished. At least, that's my best guess.