All that bug fix did was load public dependencies. I had run into this issue when making my own callbacks which failed for a while until I realized listeners weren't being loaded, I made them load in a "lower" way than XenForo has with this fix. If it is failing I would assume a dependency loading is failing.
You can try my method of loading in the listeners instead by commenting out lines 12 and 13 in root/payment_callback.php and then under that put in...
The XenForo way will run that code above however not all the other dependencies they run which could possibly be causing the issue. If it works after that then you have your issue. The XenForo way will also fire the init_dependencies event so an add-on could also cause the issue.
I'll be changing my callback to do it the same way as XenForo does when I have a chance to test (PayPal callbacks take forever to test). If I run into problems I'll be sure to share.