Oh, here's my info:

What version of Zen Cart? 1.3.8
What addons/patches are installed? Custom code to have quantities for attributes, USPS one click, sales report, Google Analytics, and since we discovered this the View Stuck PayPal Orders module which has saved my life when coupled with an email filter*
What currency are these transactions in? USD
Which PayPal module are you using? Paypal IPN

*I have a copy of the order confirm emailed to me and have enable a filter to flag and alert me when those emails contain any of the following "$1," "$2," or "$3," which catches anything in the 1, 2, or 3 thousand order range (so far anyway). Then I go check PayPal. If an order has been paid, I go find the order in the View Stuck PayPal Orders and push it through to the database.