[Steve Tinker]

Try resetting the ECU base parameters, though rain water in your "black box", mounted I assume, under the passenger seat (RHD cars) won't help, but thats usually for the security / central locking system.

1) Try disconnect battery again after removing ignition key.
2) After reconnecting battery, put key to IGN so dash lights up - but don't start engine.
3) Leave in this position for ~60 seconds.
4) Switch off ignition and remove key for ~ 10 seconds.
5) Start car as normal - the base parameters should have been reset.

If problems still persist, hook up a code reader (Durametric or equivalent) and trace fault.