The Quartus® II software version 9.1 may incorrectly generate programming files for designs targeting EP2AGX45 and EP2AGX65 Arria® II GX devices. This problem may occur when you program your device with the Quartus II Programmer or use the following file formats: .pof, .rbf, .hexout, .ttf, .rpd, .jic, .jam, .jbc, and .svf. This problem causes functional failures in some devices after programming.
To resolve this problem for the Quartus II software version 9.1 download and install the appropriate patch from the links below, and then regenerate the required programming files and reprogram the device. Note that the .sof files created during compilation are not affected, so recompilation is not required. This problem will be corrected in the future version of the Quartus II software.