I've had problems at the consignment store lately too, but only since I maxed the inventing skill. At first, I thought it was a glitch and restarted my game, but everytime I clicked the cash register nothing happened. Then out of curiousity, I cancel my consignments and got everything back. Then I clicked on the register again, and the buy menu popped up and I was able to consign everything. It has happened a few times since then. Also, there is something on that cancel consignment menu I don't quite understand. I think it might be a time limit on how long an item can stay there, but I'm not sure.
Hope that helps.
A'tuin.