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I've owned my 2006 F-250 Diesel for the past year and this "phenomenon" has happened twice, once 6 months ago and once the other day. I normally run the HVAC on "auto" and let the truck do the work. The other day it was nice out and I opened the sunroof while the HVAC was on "auto." I noticed that the fan speed went up dramactically and no matter how I adjusted the temp, it would not back down. I tried switching to "manual" and using the fan control that way, it wouldn't respond. When I tried to shut the whole system off, air would blow through the defroster at a high rate and I couldn't get it to shut off no matter what I did. Eventually I put it back on "auto" and continued to regulate the temp accordingly. The fan speed still seemed very high, regardless of what temp I had it set on. The fan speed stayed high for about 2-3 days, when I started the truck up, it would be blowing. Then yesterday, I got in started it up and the fan speed seems to have slowed down to normal. Has anyone else experienced this? Like I said, this is the second time this has happened since I've owned the truck and there's nothing in the manual about it. Any and all help is greatly appreciated.
It sounds like it could be the blower control module. You'll need the powertrain and emission control manual and the shop manual to diagnose the problem for sure. If you follow the steps in the manual it's fairly easy to do. It's just a PITA.