I've only just brushed over the posts in this thread but I have a question for you:
Do you have an immobiliser fitted?
They can cause VERY unusual illogical behaviour that is sometimes extremely difficult to spot. My girlfriend's car had one hidden inside and it took us 2 years to suss it out. Once I tore the bastard out everything was fine and has been ever since.
My advice is if you DO have an immobiliser, disconnect the power to it. Working out electrical gremlins without it attached is easier also.
Bookmarks