> I have only seen it pop-up once- for a cert that I had just issued a second prior. The cert was logged properly and the page loaded another second later.

Hmm. Possibly a timing issue? It is conventional to slightly "back date" certificates so that they claim to have been issued an hour ago, as obviously if users forgot to adjust a PC for the clocks changing your site should still work & it was seen as easier to just back date the certificates. However for SCTs because the log has a Maximum Merge Delay conventionally set to 24 hours - so such back dating gives you 1 hour less to fix any technical problems - if you miss that 24 hour deadline you're out and must start over. So we do not back date SCTs.

Thus if your system had the time slightly wrong (say, off by 10 seconds) but had Transparency checks enabled I can imagine it would reject a freshly issued cert because the certificate says it was issued almost an hour ago but the SCTs are in the near future.