I had a similar problem in my 33 ages ago, except that mine would wind up but not down so it was a pain more than anything else.
Anyway, mine ended up being a dry solder joint in the black box that contains the relays. An auto electrical mate (Chris Rogers, who posts on here actually ) diagnosed and fixed the problem, for a total cost of $0.
In your case though, if the box is clicking the relays are actually working, so the problem sounds like it's somewhere between the box and the window motor/mechanism. Get a multimeter onto the motor if you can reach it, and see if the voltage is getting that far. If it doesn't, there's a break in the wires. If it does, you either have a fried window motor or a stuck mechanism. It should be easy enough to work out which based on whether the motor seems to be "trying" to work or not.
FYI the box controls the auto up/down function.