One thing I noticed is that when running LabVIEW as the shell, the Aero theme doesn't load (I'm guessing that is a service started by Explorer). So if you develop with Aero turned on, then deploy where it is off, many fonts will be wrong. And it is likely your controls in the windows won't line up right.
My fix was to let Explorer start (starting Aero) then kill it with my LabVIEW application. This also will kill any shortcuts like Win + E, Win + D. I never tried but it is likely you could just start the right theme service and have it work properly but I never tried that.
EDIT:
I also found that command to allow operators in the Users group, access to write files.