Like Rob said, there's nothing wrong with Stencyl 3.0 specifically. It's the migration from 2.x to 3.x that causes the problem. You need to understand, 3.0 was a MAJOR overhaul of the program. Even though the aesthetics are the same, the back end of the program has been basically rewritten. They're using a completely different flash engine now, too.
I hate to say it, but you may need to restart from the ground up. Or just roll back to 2.x and finish your game without the feature you were trying to add with 3.0.