It is not a race of which team will run to his base with other side's flag. Your flag must be returned to your base and spawned there for you to be able to cap.
---------- Post added 2012-05-13 at 10:32 AM ----------
Oh and for the possibility that I misinterpreted your post; cyclone prevents the efc to cap for sure. Not exactly sure but sheep/hex/stun might also be preventing, however rooting in cap range doesn't prevent capping.
Cyclone prevents it. Cyclone makes you 'immune' to everything (apart from spirit link, oddly). Mind Control MIGHT stop it. I don't know if fears/disorientates stop it.
The bug where people can't cap when standing on the flag is just that, a bug. I don't know what causes it though, maybe someone else does.