quoted

However when I attempt to access FPGA memory my mmapping it in  
userspace the read hangs. The same happens in kernel space. Does it  
happen because FPGA memory is marked as disabled, or because FPGA  
code is doing something wrong ?

Can you access the device in u-boot?  That would possible tell you if  
the HW is functioning or not.

quoted

Another question is what can cause PCI device memory be marked as
disabled.

Good question, no idea how lspci decided to print [disabled].  Take a  
look at lspci source and see :)

Maybe the memory enable in the PCI command register isn't set ?

If you don't have a kernel driver that sets it (by calling
pci_enable_device) and u-boot doesn't set it then it's going
to be off and you'll get hangs or machine checks trying to
access the device...

Just an idea...

Cheers,
Ben.