I spent a little time today trying to figure out the .sce format, to see if I could debug the events stored in the scenario file that were not (apparently) reported correctly in either the Game XML or the Event Editor. I did not have any luck. It is a noisy format, with lots of change between saves even when nothing is touched. This is great to minimize/prevent tampering of competitive games, really annoying when trying find and fix a problem! The events themselves, or at least the news text of the events, is obfuscated so I can't use the text as a crude "counter" of active events.
I also used TOAW 3 Scenario Viewer to try and figure things out but the .NET code terminates at a dll that reads the scenario file. This dll returns the same messed up (again, apparently) events as the XML dump, which implies strongly that the XML dump and dll share the same bug, if there is a bug. Either way, it appears the game itself interprets the events differently than the visualization code.
Anyway, there doesn't seem to be much else I can do without input from those with access to the game code. I'll reiterate that I'm happy to help debug this at whatever level is most convenient (QA, code reading, code writing, etc).