I tested the plugin and Autoptimize does not cause any issues with the default settings. It is possible that with your settings it does cause issues with Transient expiry. Uncheck the “Disable transients” option again as it creates a lot of overhead to the plugin.
I would recommend the standard procedure for such cases: deactivate all other plugins, then check if the balance updates. Once you determine that the plugin works with all other plugins deactivated, then you can activate some more plugins, then a few more, until you find out which one causes the problem.
If you do find something, I would be very interested if you could share your findings. A lot of people have reported issues due to transients not expiring properly, but none so far has the technical expertise to debug the issue, and I cannot recreate these conditions on my machine in order to investigate myself.
If I knew what can cause transients to persist after their expiration time, I would be able to make the plugin detect these conditions and warn the user to take appropriate action. If you are using memcached or anything that uses a server-side key-value cache, or otherwise messes with transients, then these are your suspects.
Looking forward to your reply if you do find anything.