@dgilmour77 , I have the same problem with a configuration similar to yours. I cannot recall it for sure, but I think DynDNS worked OK in dual WAN prior to release 2.4. Pfsense documentation advises us to use GW groups as interfaces for DynDNS, but doing so has the effect you have described.
I wonder if something like that happens with dual WAN load balancing scenarios, i.e., although both WANs may be up, traffic will only flow through one of them.
BTW, as for the DynDNS situation, I am using the workaround suggested by @viragomann.