I've seen four reports (so far) of people having display problems after the last update. In all their cases they had a external monitor which showed up in the Displays preferences with only two (incorrect) resolutions. In all cases all these people did was update thier working systems.
Although yours is a different problem I am beginning to suspect that update affected video in a number of adverse ways. I think all you can do at this point is revert to a system prior to the last update and wait for some future update. Perhaps send feedback to apple.
These were not even Thunderbolt related.