Why I Hate Travel Agencies

I'm a very frequent business traveler and most of the time I book my flights using an online service like Expedia, Travelocity or Orbitz or the airline's own website. But sometimes, when I'm traveling on someone else's nickel, my host requires to me use their travel agency and it's almost always a bad experience. My bad experiences have been so frequent that I usually ask if I can make my own arrangements and be reimbursed but sometimes that's not an option.