This is not a port/protocol issue. IPS is a website... so it would use TCP 80/443. If this was a basic issue like that, you would not even be connecting to the site whatsoever.
If you put a WAF in place, you're going to have literally hundreds of rules. These all vary from WAF vendor to WAF vendor. There is not a central "WAF rule database" to say you should specifically override and allow rule 990294 and 100111. This is basically you decided to hire a security guard to sit in front of your website. The website (IPS) is not aware of that guard. Who they allow in depends on what you tell them to.
Sometimes out of the box rules don't behave the way you expect them to... this is called a false positive. You would have to either look in your WAF rules to see what is triggering and create an exception, or turn it off. But again, IPS does not even use your WAF to know what rules it has, how it is configured, or what needs to be allowed.