This is a constant problem for me. My company requires that I book with their assigned travel agency. My travel schedule changes quite often - a lot of times I'll have to change an outbound or return portion of my itinerary *AFTER* I've been cleared for an upgrade.
But if I ask my travel agent for a change, they say that they have to reprice the ticket, thus causing my confirmed upgrade to be null and void. Once the agent has re-ticketed me, I have to call UA to get back onto the waiting list
When I try to call UA and ask them to make the change, they tell me I have to do it through my travel agent... *sigh*