For some reason, when I make large changes to file structures outside of PHPStorm[version 5 and EAP6] - this can cause PHPStorm to drag when I switch back to it.
As an example, I use submodules in some projects and I find it easier to maintain them through Smartgit. So if PHPStorm has a project open, and I go and pull a new set of code for the submodule - when I click on PHPStorm to bring it back to the foreground it seems to do a check of the files and then kicks off a re-index and freezes until the re-index is done.
I'm running on Ubuntu version 12.04 with Oracle Java 7 installed. What's really odd is that it doesn't matter how much time between the file changes and going to PHPStorm - even if I do the update, do some other tasks, and then go to PHPStorm an hour later - the file check is not done until PHPStorm actually gains focus. I would have expected that through inotify magic PHPStorm would be updated immediately and run it's tasks in the background.