The the user logged in on the pc is an administrator, but for some reason although the update tells me its done, the files are not in fact installed
The files will be installed for the current user's app data folder. Let's say you're running as a limited user and wyUpdate requests elevation to an admin user. When the update is installed the files will be installed to the *admin user's* appdata folder (*not* the limited user's). Does that make sense?
If your main app files are being stored in the AppData folder, then just add your files to the "Your program's folder" in wyBuild. Now, when your user updates your app, whether they elevate or not, the files in the %appData% folder will be updated.
Does that make sense?