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Hopefully you haven't already tried a soft reset. Try it with the card out and with it in.
If that doesn't help, it may be time for a hard reset. I know that is extreme, but it seems that some driver may be messed up, and the only way to clear that easily is to go back to 'factory fresh'. Be sure you understand the ramafications of a hard reset and backup as appropriate.
If that fails to restore your CF capability, it would be a hardware issue, and given the age of the 540, could be a sign to get a new PPC. Fixing it may be more expensive.
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