My guess is some sort of grounding issue, but I figured I'd ask here first in case anybody has run into this before.
If the outside of the antenna connector is making contact with the aluminium case, that could be the cause of your issues. As soon as the RPi starts doing stuff it could be coupling all kinds of electrical noise to the case. I'd try electrically isolating the antenna connector from the case. For testing purposes you could probably simply unscrew it and make sure it isn't touching the case with any exposed metal parts. If that does solve the issue, for a more permanent solution you could for example try enlarging the hole in the case, inserting a rubber grommer and mounting the connecter to that grommet.