Could it be the repackaging?
Nope. But what could be is that the default settings used by the deployment wizard, could be different from the default settings used by the native installer.
Please compare the settings between RealVNC installed via the deployment wizard and RealVNC installed by the native installer.
But in any case, I recommend you to give TightVNC a try. Since RealVNC 4.1.3 Free Edition is not compatible with Vista/Windows 7, we considering removing ability to install it via the deployment wizard.