That one is tricky... without seeing the issue in action, or being able to dig into all your interconnected systems it's very hard for us to help...
I would suggest if you can, temporarily add one of your office IPs, or some dedicated IP that you can test from, and actually go through the site with the "IP Authentication" (surely your QA or Dev team must have a way to test that functionality is working), then see if the problem is the authentication method, or something else....