Critical Issue
An intermittent PCIe Gen2 Hard IP link-up issue may occur in Quartus II version 13.0SP1 and earlier. When using the hard reset controller in a Gen2 native configuration, the Stratix V Hard IP for PCI Express MegaCore function may incorrectly transmit at 5 Gbps instead of the 2.5 Gbps data rate during link training.
For Gen2 configurations that do not use Configuration via Protocol (CvP), follow the instructions in Knowledge Base Solution for a workaround. For CvP Gen2 configurations, contact mySupport.