This issue has been resolved offline. The problem was caused by me altering the blackberry-nativepackager.bat to meet some custom requirements for my studio. I hadn't realised this file would be used for the debug token stuff in the IDE.
I don't think this problem is going to be applicable to anyone else so I don't provide any further detailed information, apart from suggestion if anyone else has a similar problem, try installing the SDK freshly to see if it fixes it, as this would have resolved my issue straight away and highlighted there must be something wrong/weird/different with my previous installation.
Best regards,
Steve
