There are many things going on in Progress Report 11 so I will touch on a couple of them.
One of the things that Charlie is having difficulty with here is that he has found out that people were making fun of him at the factory. This is very hard for him to deal with because he is realizing that he has always been easy to pick on and make fun of. Instead of calling in sick he could have gone to work and confronted those who were making fun of him. They may have then just left him alone or there could have been a big confrontation. Charlie does not like confrontation so I believe this is why he avoided the problem.
Another issue going on in Progress Report 11 is that Charlie realizes that he has fallen in love with Miss Kinnian. He is noticing that she is very beautiful and he is attracted to her. He is becoming very smart and I think this scares him. Deep down he knows that there is a chance he will become "dumb" again. He could pursue a relationship with her. The problem with this is that she may turn him down. If she doesn't turn him down, there is still the possibility that his progression will reverse and he will become the same old Charlie that he was before making the relationship impossible.