Reading to and writing from the MSI-X capability registers for the the Altera® PCIe® Hard IP core may not yield the expected values when you progam the device with programming files from the Quartus® II software version 9.1 or earlier.
This behavior is caused by a problem in the Quartus II Assembler. A patch is available to fix this problem in the Quartus II software version 9.1.
Please download and install the appropriate patch from the list below, then rerun the Assembler and reprogam the device with the new programming files:
This problem will also be fixed in a future version of the Quartus II software.