I seem to have the same problem: the magnet in the lower right part of my cover does not seem to be strong enough - it is the right way in (checked it with another magnet) just not strong enough to attach to the flap magnet.
My solution: get some thin super stron neodym magnets and stick them to the magnets in the flap - they stick very strongly to the magnets in the flap and have enough power to hold the flap closed no matter what.
I was thinking about glueing the magnet to the cover but they seem to stick good enough without it.
I got them
here.