Hello,
It sound like your registry might be corrupt. Are you having problems with other Software Packages?
If not, you might want to un-install, then re-install TestStand.
What about the Operator Interfaces, are they working? If they work, the TSEngine should be ok.
Do you get the error when you start TS? Or when Executing? Which files did you loose?
TS uses "National Instruments\TestStand 3.0\Cfg" to get configuration information when loading, so you defenetly need to make sure your desired info is there, else new, mostly empty files will be created.
In any case, I would defenetly suggest to re-install TS if the problem persists. Else, you might give a registry cleaner a try. I have had a good experience with RegCleaner 4.3 which you can download from the web.