eliminate1337

I'm having issues with 1.0.2. The game seems to think that the warp bubble counts as some sort of fairing or service bay, and doesn't let me activate engines within the bubble, even when the drive is deactivated. The error message is "cannot activate engine while stowed". It can be fixed by undocking then re-docking whatever part has the engine on it but I'd like to know if there's a fix. I have a ton of mods installed but all through CKAN so there shouldn't be any incompatibilities. Maybe it's procedural fairings breaking it?