Have you tried removing and re-installing since you upgraded? That’s all I could suggest.
Yeah, it was a totally fresh install of Mint 16 Petra. When I tried to upgrade from Olivia to Petra the whole thing died.. the joys of Linux :)
In the end it pushed me to figure out how to use PhpStorm’s built in “file watchers”, which turn out to work awesomely. So… goodbye Koala!