Has anyone ever had Avalara report two different tax amounts despite the subtotals not changing?

Yes, but not without reason (sitting for some time and re-calculating) or change to address, addition of exemption etc. etc. - Many variables in play. If you are sure nothing changed and you get different rates you can check the avatax subtab on the transaction and see what was sent to the service as one example, you can also look up both in backend and see if something changed there (addition of a state in your setup, or similar.) You can ask avalara support if it really seems like it a bug, they have additional logs much like Netsuite support.

@PWN thanks for the input most of those we looked at in the interim, much appreciation regardless!