I've got a CLE that I've used extensively, but I've never had that problem crop up. Any chance that when you return to AE that rather than setting to the "neutral" setting, you are dialing in some exposure compensation?
Otherwise I'd say it's a job for the repairman. Luckily the electronics are heavily based on Minolta XG technology (or so I've read), so a competent repair person who knows how to open up the CLE should be able to work on the electronics inside.
If you have any luck with a repair, pls post that info here. It'd help us other CLE users. Thanks.