This error may be seen in the Quartus® II Software version 9.0 SP2 when programming a design security key using an Encryption Key Programming (.ekp) file with tamper protection mode enabled.
The security key may be programmed correctly, but the following false error messages may be issued by the Quartus II programmer:
Error: Verification failed for device number <number>
Error: Operation Failed
The Jam/JBC and SVF programming flows are not affected by this problem.
A patch is available to fix this problem for the Quartus II Software version 9.0 SP2, download and install the relevant patch from the following links:
Download the Quartus II 9.0 SP2 Patch 2.11 for Linux
Download the Quartus II 9.0 SP2 Patch 2.11 for PC
Download the Readme for Quartus II 9.0 SP2 Patch 2.11
This issue is scheduled to be fixed in a future version of the Quartus II Software.