Thanks Mike,
That article did help in a stepping stone kind of way. The original link didn't provide any solutions, it did however have someone talking about 'Permission Denied' Errors. A googly search on 'Permission Denied Visual Pinball' led me to an Pre-Vista application called CACLS. The successor being iCACLS.
My folder structure is 'C:\Pinball\PinballX' and 'C:\Pinball\Visual Pinball', so I ran these command in sequence from CMD:
icacls "C:\Pinball" /inheritance:r /grant:r Administrators:(OI)(CI)F
icacls "C:\Pinball" /grant:r Administrators:(OI)(CI)F /T
icacls "C:\Pinball" /grant:r Administrators:(OI)(CI)M /T
From what I understand, these commands change the NTFS permissions on C:\Pinball, removes all existing inherited permissions and replace with Full control for everyone and Change/Modify permission then applies the new permissions to the folder and inherit down to subfolders and files (OI)(CI).
This did have a positive effect. When the table loaded, it was at the top layer of the overlay. GAME ON!!!
New problem now. When the table is exited from, PinballX does not reload into the table selection menu of PinballX and remains as a black screen. ALT-TAB doesn't work. When forced closed, it reloads itself after 5-10min and the table selection is no longer in cabinet mode, but in the standard windows resolution and orientation. Only after a whole system reset, does the system recover.