I have had the same kind of problems with AGP slots,
sometimes you have to move your card about a bit ,usually if your
mother board is oldish, ive not used the newer e-pci cards,its normally
the socket that gets a bit loose over time.
I mount my motherboard upright, where the jamma board should be ,with a base from an old pc case and slots to sit the bottom of the card in, then use screw in metal hooks to go through the screw hole's to hold the base in place, it works really well and is solid.
Take the board out of its case if you suspect your card wont fit properly and then try it, its most likely the socket,try it in a different motherboard if you still have problems.