Well, then there are three things to check out.
1. Check if the device is having SBIOS requirement to limit MMIO addresses to 42-bits. This can be confirmed by checking the vmkernel logs for messages like
2013-02-17T12:20:07.184Z| vmx| I120: PCIPassthru: 0b:00.0 : Device BAR 2 requested 64-bit memory address that exceeded MPN type (66038343401472).
2013-02-17T12:20:07.184Z| vmx| I120: PCIPassthru: 0b:00.0 : Device BAR 4 requested 64-bit memory address that exceeded MPN type (66037269659648)
Or,
2. Check if your card is having ACS capability. This you can confirm by looking at the vmkernel logs for messages like
PCI: ssss: nnn:nnn:nn.n: PCIe description
PCI: ssss: Not a ACS capable device
more info of this at here
3. Worst case, you are also one of the victim of 5.1 Passthrough being broken. Join the clan here