What version of PyroSim are you using? I just learned that versions of PyroSim 2010 prior to 2010.2.0111 had a bug that caused exactly the problem you are describing. In January 2011, we released a patch. You can see the release note here:
http://www.thunderheadeng.com/2011/01/pyrosim-2010-2-0111/If you have a more recent version, then we must have missed something and need to release another update. Message or email me for download instructions if needed.