I'm running the latest version (1.3.9h) and just recently I had a strange order appear which was generated by notify.paypal.com
It should have been appended to a previous order, but it wasn't.

An order was placed in Australian currency (our primary currency is CAD, but AUD is one of the options we give). The PayPal status returned and logged under that order was:

Payment Type: Credit Card (WPP)
Timestamp: 2011-04-21T11:07:42Z
Payment Status: Completed
AVS Code: G
CVV2 Code: M
Amount: 69.76 AUD

Then 17 seconds later, in comes a blank order from (notify.paypal.com) listed as Payment Method: Gift Certificate/Coupon with this status:

PayPal status: Pending multi_currency @ 04:07:41 Apr 21, 2011 PDT
Amount: 69.76 AUD

I replaced the actual transaction ID above with XX's, but they were identical. It's obviously a status update on the previous transaction, but was not updated to the original transaction and instead created a new one. Is it because the second transaction says "Trans ID" instead of "Transaction ID"?

PS - I'm using the latest version 1.3.9h

Related thread:

I can provide more details if needed.