Vista icons in the windows file explorer do not work to show they are PHP files.

In the registry PhpED_File it shows this for the default icon:
"C:\Program Files (x86)\nusphere\phped\phped.exe",-11

PhpED_File is not the entry that links .php file extension with particular icon in phped's resources.
Please check HKCR\.php and you'll see who grabbed the association. Probably it's ioncube.

To restore associations established by PhpED, please run cmd As Administrator, and run phped in the console with -RegServer command line argument.
Alternatively, you can right click on the phped\debugger\register.bat file and run it through Run As Administrator menu.
Note that running as regular user (not administrator) won't change HKCR values!