When trying to autocomplete code or open up the dropdown menu's the window / dialogs will appear for a short time and then get hidden behind the main editor window.
The problem is related to java window handling in tiling window managers such as AwesomeWM.
To solve this see the answer below.
You need to edit the VM options so window hinting can be done correctly. I installed PHPStorm under /opt/phpstorm (linux)
Edit:
bin/phpstorm.vmoptions
bin/phpstorm64.vmoptions
Append the following line:
-Dide.expansion.hints.enabled=false
Restart phpstorm and the problem should be fixed.