We are having a similar problem starting from June 4th in Azure. Our app is hosted in an AppService running IIS. Not sure if it will help, but here is where we are at:
After talking with both Cloudflare and Microsoft, we have come to the conclusion that Microsoft is actually throttling traffic from cloudflare to the Azure stamp we happen to be running. This throttling is causing the intermittency. The stamp is an Azure backend concept (it’s a collection of ~10 servers, shared across customers/tenants in a given region) that we have no control/visibility over and for some reason Microsoft chose to implement DDoS throttling is at this level using IP or similar routing rules. This is a problem as some other Azure customer is inadvertently triggering Microsoft’s rules to throttle all Cloudflare traffic, including ours. We are being told to try lots of tricks in hopes that a new stamp will be assigned. No luck yet.