Aye, something doesn't "feel" right for sure. Everytime I try and run a more modern core, I wind up back on 992. I do get spikes (on Windows) where a zone goes to 90%+ CPU for s moment, with nothing happening in the logs at all. I have avoided Linux altogether since 992 since the entire system tends to crash (kernel). So who knows. Maybe you can do a diff on the last version that worked for you against the new source, see what changes were in zone files...
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