If you maximize PHPRunner and then close it, it improperly saves the window size to the registry as the maximized size. It should only save the window size if the state of the window is not Maximized or Minimized.
The worst part of this, is if you minimize PHPR, then right click in the taskbar to close it, it remembers the window size as, well, nothing, and you've now lost your PHPrunner. It shows up in the taskbar but you can only see the window if you maximize it.
To fix this, if anyone runs into the problem, delete the registry value -
HKEY_CURRENT_USER\Software\XLineSoft\PHPRunner4.2\WindowPosition
And then you can have your normal window back.