Yes, there is known problem with the verification operation in the Stratix® III design security feature using the Serial Vector Format (SVF) file generated by the Quartus® II software version 7.2 SP2. The post-programming key verification operation in Stratix III design security SVF files always reports the error “Non-volatile key programming failure with .SVF file” regardless of the key programming outcome.
To obtain a workaround for this problem, submit a Service Request via mySupport requesting the Stratix III design security workaround for the Quartus II software version 7.2 SP2.
This problem is fixed beginning with the Quartus II software version 8.0.