It kinda hard to give you a list of modules and modifications since the site is modified. The question remains, why all of the sudden when nothing have changed as far as the site goes. The IPN start acting up, then the Express Checkout which is suppose to function similar to Authorize.net is acting up too.
Couldn't be something that PayPal has changed that maybe Zen Cart didn't catch up to.
The looping isn't all the time so testing it on a test website doesn't give accurate results. I try to test it myself and was able to checkout but that doesn't mean the few customers that called are making it up either. I didn't give it much attention the first time a customer complained but when I had 2 people call back to back with the same claim, I took a look at it but no issues for me.
The only change I did was enabling the Free Shipper module, but the issue appears on products that the Free Shipper rule doesn't even apply to.