You can get verification errors with the Quartus II software version 5.1 programmer if your flash device is not erased when you program it with a new design. The programmer in version 5.1 does not automatically erase the flash device before programming. You must check the box for the erase function to perform a flash erase before programming. The programmer does not allow you to check the erase and program box at the same time.
This problem is fixed beginning with the Quartus II software version 6.0.