This is the first post I've seen that offered any real help with this issue, which I too suffer from. Hopefully I can get it to work.

I tried following the steps recommended, but something really strange happened ... my Rules came back after deleting them and the mail rules plist and the plist back up and emptying the trash and restarting Mail.

Any clue as to what might be happening?

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Do you have .Mac syncing turned on? In which case make sure you aren't re-syncing your old rules back.

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Did you quit Mail.app before removing the plist file ? If not, I think Mail.app will recreate it as it was.

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