Yes, due to a bug in the Altera® PCI Express IP in Quartus® II software version 9.1SP2 and earlier, some systems may either downtrain to a x1 link or fail to initialize.
A patch is available to fix this problem for the Quartus II software version 9.1SP2. Download and install patch 2.18 from the appropriate link below.
Quartus II software version 9.1 SP2 Linux Patch 2.18
Quartus II software version 9.1 SP2 Windows Patch 2.18
This problem is scheduled to be fixed in a future release of the Quartus II software.