My character put 1001 gold in an account at the Elite City Bank, but when I returned later that day the account said 1 gp.

Any thoughts?

Is this including the initial 1000 gold charge paid to open the account but not deposited into it?

That might be it.

If you lose that initial deposit of 1 K, then it's all good.

I just went in game to double check, the account creation fee is 1000 gold. So Mr. Gwydion, if you deposited a total of 2001 gold, then you certainly are missing 1000 gold. If you deposited 1001 gold, in total, then I think your account balance is just right.

Sounds like it worked exactly like it is supposed to.