Man that was easy! Edge condition on filter list, the last one in the list. I obviously didn't test with a plan having the last filter in the prefs list in it! Bad enough to rate a maintenance release, 4.1. One line fix, easy to verify, so it took only 30 min total (release notes in help doc changed too).

http://download.dc3.com/ACPPlanner-4.1.1-Setup.msi (just run this, don't uninstall)

http://gemini.dc3.com/Gemini/Default.aspx?p=21&i=318 (issue tracker record)