Are your errors specific to the 2 Flash files you mentioned, or do all/any SWF files exhibit the same issue?
Is it the Director file? Can you import these 2 SWFs into a new/different Director file?
Thank you for your reply! After some further testing last night we had a few breakthroughs.
The behavior of the SWFs in general was fascinating, the other flash files originally in the project were fine until we brought in these two new ones. So we took a look at the new SWFs themselves to see if something weird was going on. The new files were made originally in Flash CS5, but we also tried them in CS4 to see if that would help. No dice.
Bringing them into an empty Director 12 project caused an instant fatal crash as well.
We also tested in Director 11.5 both in a populated project and an empty one. Same fatal error.
We also tried Flash CS6 and tried remaking the SWFs in that version, thinking that might play nicer with Director 12. Same problem.
Finally, we took a closer look at the Flash Player publish settings for the SWFs themselves. They would default to Flash Player 9. We tried moving the setting back to Flash Player 8 and republished.
Importing SWFs back into Director was at last successful and functioned normally. We also tested this with SWFs made from CS6 and CS5, both worked as long as we put the publish player back to 8. We have tested this in Director 12 and 11.5, the SWFs seem to behave now, but we will continue to test to make sure and I will follow up if anything further develops.
I hope this was helpful to anybody else experiencing this strangeness, it feels like a weird glitch for sure.