Due to a problem with the PCI Express® core implementation in the Quartus® II software, the Deassert_INTA message may be sent out shortly after the Assert_INTA message, while the Rxmirq_irq[n] signal is still asserted. This is not the intended operation of the legacy interrupt logic.
This issue affects designs implemented in Qsys, starting with Quartus II software version 11.0.
To workaround this issue:
1. Download the following file:pciexp_dcram.v
2. Copy this file to the following directory in your Quartus II installation directory: <install_dir>/ip/altera/ip_compiler_for_pci_express/lib
3. Regenerate the PCI Express core within Qsys
4. Regenerate the Qsys design
5. Recompile your project
This issue will be fixed in a future release of the Quartus II software.