Is this the first time the fan has been working? If not, the question is why it would start doing this with a different controller. I can't imagine why a controller that's not the right part number for your car would create the sort of mechanical noise you're describing, but I suppose it may be possible.
BTW, there are cheap rebuild kits for controller screens that are very good. I've done it myself.
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2001 Boxster, 5 spd, Seal Grey
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