Due to a problem in the Quartus® II software, the Design Space Explorer may return unknown values when compiling designs targeting Stratix® II or Cyclone® II devices. This problem occurs when the Design Space Explorer attempts to use the deprecated Classic Timing Analyzer instead of the TimeQuest timing analyzer.
To work around this problem, add the following assignment to your Quartus II Settings File (.qsf):
set_global_assignment -name USE_TIMEQUEST_TIMING_ANALYZER ON
This problem is scheduled to be fixed in a future version of the Quartus II software.