Samson, I have had the same problem - I was trading EUR (order was placed with Excel but I watched it activate in TWS). I had the stop in (not stop limit) and I watched in disbelief as the market ran past it. I had to manually close the order for a sizeable loss.
I sent them an email explaining what happened, with the order id #, and this was my reply (after 7 days):
"If such a problem occurs again please call the Trade Problems desk at 877 442 2757 option 2 at the phone menu.
They have access to your account and can check any orders submitted to the system.
-Ben
IB TAC"
This error, plus the frequent loss of feed, makes IB a horrible choice for API/ autotrading. I am currently looking at MB and TS accounts. I could not believe that TS has lower commisions on futures!!!