I just upgraded to from Moodle 2.9 to Moodle 3.1. Actually I installed 3.1 from scratch so that all the little mods to code were gone.
So, to get the Atto equation editor working again, I again had to change the timeouts. I changed the 500 ms timouts to 5000 in these files:
It did fix the problem (again). But I mention this because I feel an increased timeout should be incorporated into the standard Moodle distribution. 5000 ms might be tooo long, but 500 will be too short for many users.