I have added two of the three missing indexes using phpmyadmin. When I try to fix the mdl_tag_instance index, I get the error below. Fixing the two tables did not clear the slow query.
#1072 - Key column 'tiuserid' doesn't exist in table
In a reply below, I commented that if I remove an affected account from all courses, the slow loading goes away. I added an account back to the meta enrolled courses one by one using manual enrollment. The slowness did not reappear until the account was in 7 courses. Then the My page too about 15 seconds to load. Adding an 8th course increased the load time to 35 seconds. It did not matter what courses they were. It just mattered how many.
I have more than 2000 staff that are enrolled in the same staff courses through the same meta course. Only seven have reported experiencing the slow query. Even If I delete an account, it is slow if I create a new one with the same username. New account that have never been in the system work fine.