Due to a problem with the Altera® Hard IP for PCI Express® in Arria® V and Cyclone® V devices, toggling the cpl_err signal will not log the error in the Error Status registers. This issue affects all cpl_err[*] signals, but does not affect the cpl_err_func signals.
Application Layer logic must perform an LMI write to the appropriate error register, and create the appropriate TLP, to workaround the issue described. See Table 2-29 Completion Status Field Values, in the PCI Express Base 3.0 Specification.
This problem is not scheduled to be fixed in a future Quartus® II software release.