I have what at least superfically seems similar.
Summary: I have a simple model database which is stuck due to an overfull transaction log - can't add more log space or another log file, or do much of anything, because it is stuck with a wait on 'CHECKPOINT'.
(Actually I have half a dozen in the same state, but I'm only concentrating on one, trying to find a solution.)
(My only guess is that it filled the log when there was no extra disk space, and some flag got set saying it is hopeless, and now I can't get that flag unset.)
I have a simple model database with a full transaction log (over 100% full). I have plenty of free disk space and the log is set to autogrow by 10% - the log file is c. 800MB and I have 20G+ free, so it growing by 80M should be quite possible.
Yet the log file won't grow, and I can't add another log file, and I can't adjust its size.
Everything fails with an error that the transaction is full, and the wait_desc is 'CHECKPOINT'.
DBCC OPENTRAN shows no open transactions. These are all SharePoint 2012 databases, and I've stopped & disabled the services involved (inetsvr etc) so there are no open user connections.
DBCC LOGINFO shows that I have over 200 VLFs, all in status 2 -- so it is indeed entirely full.
I can't execute a full backup (trying gives the same error - full transaction log due to 'CHECKPOINT')
(I posted a longer version of this elsewhere, but haven't received any help suggestions yet, I think.)