The system caches the requests on your end, so that's probably what you were seeing. Have they all gone through now? The caches should have expired by now.
If you go to Admin -> Analytics -> Test Setup, visiting that page will bypass the internal WordPress cache. Does that change anything there (specifically, does it show you having a Pro license down at the bottom of that page)? Also, what are your 3 domains (which 2 aren't validating)? I'll do some checking on the backend here.