I do not know what is happening in your account specially the part that you said you have 25k and IB says you only have 2500.
Was your option a multi leg order or single option order? I just guess maybe that was an all or none order which may be used to transfer positions between accounts in brokers. You can open a ticket and send them your log file and ask them for an explanation. Not to complain, but more to educate yourself on what was going on.
Straight equity short. It's not about IB saying I have less, it's IB saying I cannot short in cash, full value. Try to shorting ZGNX in your account for all your available cash, shares are available but IB won't let you, they cut the position down to something like 25%.
This is about IB's margin starting to be insanely restrictive. And no, they are not protecting me, it's about them screwing ALL the customers thinking that a few might end up causing trouble.
If you don't know what you're doing, IB is awesome. If you do know however - IB will end up costing you money.