This post today shows one solution to erratic AC operation:
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E39 (1997 - 2003) >
A/C Fan Troubleshooting
Hey guys I appreciate your help in troubleshooting this issue. I know there are millions of threads about this but I just wanted to post my solution to possibly help new users.
I bought a used hvac control unit from ebay for $80 and installed it this morning. I now have cold air and everything else including the air staying on after shut down is now working as intended.
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