We ran into this last week! First, you can turn off your internal database auto-backup to see if that helps:
Do you have normal backups turned on?
Also, how large is your config.idb file?
We had auto-backup turned off already but were still getting the internalJson and SingleConnectionDatasource errors frequently. Our error was that the config.idb file was far too large (it was 1.5 GB). We ended up having to export our projects and re-import them on top of themselves to clear out unnecessary stuff from the internal database and the size dropped to ~200 MB and haven't had any issues since.