IntelliJad 1.4.0 was just released.
Due to an issue described in
I've added the option to disable the project-closing cleanup operations while I look for a way to fix the deadlock. I hope this will at least temporarily address any issues you've had with this.
By default, the cleanup operations are enabled. To disabled them, open the IntelliJad config and uncheck the "Cleanup source roots on project closing" box.
Apologies to anyone whose day I've accidentally taken a dump in!