Permissions Issue and some programs

Have a Wins 7 Home Edition 64 bit

It had a System restore back to June 2012 - then no Undo point to reverse it

Trying to start some programs gets message :

The system could not find the environment option that was entered

SP1 will go so far in Safe Mode, but when starting in Normal Mode Fails.

So in Safe Mode, the programs will run. I ran Tweaking.com to Reset File Permissions, but seems to make no difference in Normal Mode.

Also ran Malwarebytes in Safe Mode - nothing found

Thanks