performance at -40C temp changes with minor design changes

We have a Cyclone III design that has 16 output lines we use for debug monitoring.

For example we send out chip select and other control signals to the debug outputs which we monitor with a logic analyzer.

We can operate the design down to -50 degrees C and lower. However when we remove all of the output lines the design quits working correctly at -40 degrees C.

We have the Time Quest Analyzer reports for the two different design builds and note there are more red highlighted entries in the reports however we are uncertain how to interpret the reports.

How difficult is it to setup and run a simulation so we can analyze the output signals?

Thanks for any suggestions