1. Just to be clear, you are using the bid for the short and the ask for the buy in determining that your order should be executed, right? That is, if it's:
Ticker Bid-Ask BidSizexAskSize
AMD 20.50-20.55 10x10
INTC 17.45-17.50 10x10
Sell AMD/Buy INTC needs a spread of $3.00 or less to be marketable.
2. In this example, AMD is a Reg SHO "A" stock, and so does not require an uptick. In other cases, you need to be sure that the short stock is either uptick-exempt, or that the bid price you are attempting to hit is either a legal upbid (for Naz stocks), or would result in a zero-plus-tick for NYSE stocks.
3. In the case of listed stocks (i.e. NYSE/AMEX), IB may require that the bid/offer you are attempting to hit/take be on an ECN (and probably that the ECN be at the NBBO or better and that the market is not locked/crossed), so they can be assured of an instant execution. They may possibly loosen this up for NYSE stocks if the current quote appears to be NX-eligible (allowing for auto-ex at NYSE).
I'd suggest turning on auditing (Configure->Misc->Create Audit Trail) and, if you get a situation where the order should qualify under the above guidelines (at least) and does not get filled, send a trouble ticket with the audit trail for the specific order that didn't work so they can research it.