-- UPDATE --
the new version of ideaVim plugin fixed this issue already.
I'm using PhpStorm under ubuntu with ideaVim plugin.
One thing annoying me is when I edit in the popup windows such as show diff editor I need to press Escape to switch to Vim normal mode, but the popup window still gets closed.
I can't find any settings to change or disable Escape key mapping in PhpStorm for closing the popups.
the new version of ideaVim plugin fixed this issue already.