[CREWZIN]

There's a couple of different Error code lists, not sure why.

Disregard the P1684, just plain don't worry about it.

As far as your other code, here's what PT Do-It-Yourself.net has to say:
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P0401 (M) EGR System Failure - Required change in air/fuel ration not detected during diagnostic test.

The P0401 is a very common code for the EGR. More than a few have been replaced under warranty on the PT. A new valve should cure the codes. Make sure you follow replacement instructions precisely.
Once it's replaced, the code won't clear itself using the battery disconnect technique. Have the dealer clear it using their DRB scan tool during your next visit.
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Try the dealer first and see if the EGR still falls under the emissions warranty.