I've spent time trying to determine the root of this problem.
My previous configuration had pi-hole as primary dns and both internal dns servers as alternates in my router, a 4 node Linksys Velop AC3900. The linksys firmware was last updated in Sept and is current. This configuration remained constant for 1+ years with no problems.
All 3 dns servers, pi-hole included, are VBox vms running ubuntu 18.04 on 2 different hardware platforms also running 18.04. These servers run other vm's also, such as zabbix, webmail, etc. The router is hardwired to both servers.
I have now run the pi-hole vm on both hardware platforms with the same results - that it blocks ads only when it's the only dns server listed on the Linksys router.
I have an image of the pi-hole server from 7/2020. I'm going to use it (without upgrading pi-hole itself) to see if that has any different outcomes. I am attempting to test of newer pi-hole software is just enough slower that the router defaults to backup dns before pi-hole can respond. Doubtful but worthy of a test.
And thanks for