it could be possibly:
1. some problem is the pcie slot itself. this cold be due to bad seating of the card because of less space in the cabinet.
2. maybe the power supply is not strong enough.
give more details of "not reading" the card. does the PC boot or it crashes on the desktop etc. give details.
I found that my power supply was not in fact strong enough, I had thought that it was but I was reading something else
Is there any other reason or is that the only thing i should be worried about?