I agree. This happens to me too and it is really annoying.
Every time I use MC's Facebook upload system, I have to re-authorize it. There is a checkbox on the web login dialog that says "remember me" and I check it every time, but it doesn't work.
I want the HTPC's MC to login as my wife, and my basement machine in the man-cave to login as me.
It seems to me like MC's web UI component isn't storing the cookies properly, or is expiring them prematurely, or something. When you "destroy" the web UI object, does it destroy all cookies unless you explicitly save them or something?