I just upgraded (well, I tried this a couple weeks ago too, but was too busy then to try to deal with this problem) to AIR 3.9 from 3.8. Under 3.8, my build/launch configurations all worked just fine. Now in 3.9, I get the "initial content not found" error from ADL. The mysterious thing is that if I immediately copy the adl command from the IntelliJ run box to the command line, it works just fine. This would be OK as a stopgap, except for one thing: I can't debug using this workaround. As far as I can tell, this is new with 3.9. I've used IntelliJ 12 with several versions of AIR 3.8 with no problem.
I've done everything I can think of to try to clear this up, anybody else have some suggestions? Is this just straight up a bug that needs to get fixed by IntelliJ? I don't mind submitting a bug report if that's the case, I'm just not sure yet this isn't something I can't fix locally.