I thought I would update on this issue.
Our application has been updated to include a proper UAC manifest
(asInvoker) for Vista, as well as the digital signature, which it
already had. These changes did not fix the Open File - Security
Warning prompt that our client gets when trying to run the
application.
We renamed the folder the application is installed in, as well as the
application itself and still the warning appears.
We had the client turn of UAC and the prompt still appeared.
We also had the client export his registry as text. In his registry
we found a VirtualStore key under HKEY_USERS\<user id>\Clasees\Software
\Machine\VirtualStore\<company>\<product>. Deleting this key made no
difference,