Folders not being indexed

PHPStorm 3.0.2 isn't indexing folders in a particular project of mine. Other projects are fine, although the affected project is the only one that have that uses SVN, not sure if that's relevant.

I've tried invalidating the cache and have deleted the .idea folder and opened the project again but to no avail.

Any ideas?

Cheers,
Terry

ps. Have just tried EAPs of both PHPStorm and WebStorm. Same thing in both...