Description
Due to a problem in the Quartus® II software version 13.1, you may see that compiles with identical source files do not have identical fitter results if you are using the SignalTap™ II Logic Analyzer and you have selected a state based trigger.
Resolution
To work around this problem, do not use a state based trigger in the SignalTap II Logic Analyzer.
This problem is scheduled to be fixed in a future release of the Quartus II software.