Can auto-update be disabled for the xcopy version of LINQPad 6? Seems like group policy blocks the update even for the xcopy version.
If group policy is causing issues with auto-updates for the xcopy-version, it's highly likely that you'll run into a similar problem with the RTM version. The auto-update mechanism is essentially identical - it downloads a newer version into %localappdata%\Updates6.AnyCPU and runs it from that folder. The newer version then patches the original if permissions allow.
You can block updates for both in Edit | Preferences.