I'm new here, but felt I should reply. I've been sick the past three years, and noticed similar reactions from my cats (which did get better over time), and my birds (an african grey who unfortunately died before I was diagnosed, and a conure who has just "re-warmed" up to me in the last few months).
I figure there are a few things that could be going on, and possibly a combination.
First, you are right, you DO smell different when you are sick, especially if you have a life-threatening illness. In the wild, an animal that sick is a liability to the pack or herd, and depending on the individual personality of a dog (or horse, or....whatever), they will either try to protect you, try to avoid you (to keep from becoming ill or possibly become prey themselves), or they will become aggressive to "cull" you, and remove the perceived liability.
If you also take strong medications, such as chemotherapy drugs, had surgery, which will mix strong-smelling agents such as alcohol and iodine with blood and, essentially, your "innards", or had an extended stay at a hospital, you will smell "bad" to an animal, and this can make the animal fearful, distrustful, or confused, any of which can cause aggressiveness.
Also, and I think this is what was happening in terms of my african grey, at least, you don't just smell wrong (birds have a horrible sense of smell), but you move differently, act differently, etc. You may feel better after your bath, and so move more like yourself. So, whatever body language you are giving your dog that makes him aggressive disappears, and he feels comfortable and safe with you...he may not even recognize you before the bath.
Last, some dogs, especially alpha-wannabe males when there is an alpha female (or male) in the group will try to take advantage of your poor health to work his way up the social ladder. This, too, is natural behavior, even though it is mis-directed at you as a human. It sounds like you are at least sometimes bedridden, and this is even more of an invitation to him to become aggressive, since lying down, especially on your back, is a submissive pose for dogs.
If this continues, it might be worth finding a dog behaviorist (I know that some SPCA groups offer free or low-cost behaviorist consultations) to look more closely into what is going on. Sometimes an objective 3rd party can see small things that could be changed that would make huge improvements in your dog's behavior towards you and your illness.
Good luck...hopefully things have gotten better since you wrote your post.
Michelle
