There is a known issue with some revisions of silicon for Stratix® II devices. Refer to the Stratix II FPGA Family Errata Sheet (PDF) for information about which devices are affected.
Programming file generation is disabled for designs that use M-RAM blocks in Stratix II devices in some versions of the Quartus® II software. Descriptions of this issue and solutions are available in the Stratix II FPGA Family Errata Sheet (PDF).
If you are using silicon affected by the issue with the M-RAM blocks, the following Related Solutions describe the other software features affected by the known issue with M-RAM blocks.