@Mike *****
and since you got the new passport have you filed at least ONE 90 day report in Bangkok in person?
It used to be ONCE you got a new passport inside the country you couldn't use the online system anymore because the TM6 (arrival departure card) can only be coded to one passport (the one you entered on) so it would be a mis-match in the system.
BUT now the new system doesn't require a TM6 # so I dunno why it would not go thru.
Apply again with the new system. I know some people who applied, were rejected, applied again with the exact same info and were approved 😮