When I return to town and sell my ill-gotten gains, I'm not able to deposit gold at all. I click the button and nothing happens. If I log out and log back in again a random amount of my gold on hand disappears and if I go straight to the bank, I can deposit. If I log in and go to the merchant first, I can't deposit to the bank.

Humm... does an amount of gold disappear every time you relog after killing mobs for a while? Sounds like a possible client/server disagreement.