It's just possible that your two posts may be connected, also. If you search the archives, you'll find cases of the wrong brake light bulb causing the car not to stop running, so you may have a short.
Also, the trionic limits you to base boost when the brakes are applied, and I am sure I remember a case of someone fitting the wrong brake bulb and being limited to base boost.
Therefore I'd suggest you check out the bulbs, contacts and wiring in your rear lights as the others have suggested, since this may cure your strange engine problems too!