1: Perhaps he goes to work despite being sick, because he feels he has no choice but to.
2: Perhaps he isnt sick, but sick and tired (of learning with you) and he really doesnt know how to tell you without hurting your feelings so he is using this as an excuse.
3: Perhaps he really has a hard time getting up in the morning, despite a wonderful chavrusa and chabura and he needs a little chizuk in this area.
If this has been going on for say a week or two, I would tell him straight out, that you will be starting with a new chavrusa (or looking for one depending on how close you are or how easy it is to get a new one) while he is out sick and once he is better, he can join the 2 of you. In the meantime, since it is only a couple of mornings I would go with option 1.