my friend and I would commute together to the same government building for work. He used to hang up his shorts and have a fan blowing on them to dry them out. He got counseled that having the bike shorts / fan setup was unprofessional to look at and also caused a smell and to stop doing it...
I actually found that the easiest way to solve the problem was to lay my bike shorts on my office chair (the seat not the back) and sit on them while working... I guess the combination of my body heat and the absorbtion of my work slacks worked so that my shorts were dry by the time lunch rolled around without any extra smell...
oh and my shorts are the mountain bike variety (due to it having pockets and also my own modesty).