I do not know the functionality for the IB best order so speculating here....but is it a market order? Limit order? If limit then you must be pricing it below the bid to sell and above the offer to buy or you would not get filled at anything other than the inside price via SuperSOES since SS only fills at the (current) inside price.
WHat is likely happening is that when your order goes live, the inside market is held by ECN's which the BEST order does not get to in time to match with them. Meanwhile all SS orders are being held in queue until a MM is at the inside. Then, as the ECN's bids/offers leave the inside, the new inside may be 4 or 5 cents or more away from the old one. Assuming there is a MM there, all SOES orders held in queue begin executing against that quote. This happens to me fairly frequently in fast moving markets and is a downside to a SS outside limit or market order.
For example, market is 50.00 x 50.02 with ISLD and BRUT at the 50.00 bid. I route a SS market sell order which will sit there until a MM comes to the bid. If a MM joins ISLD and BRUT at 50.00, I get filled at 50.00 (meanwhile I may also be trying to get the ECN volume at the 50.00 bid simultaneously but that's another story).
I price the order at market (or below the current bid say at 49.95) to keep my place in line in the SOES queue in case the ECNs pull quickly and the stock starts to drop....ie I want to be the first one to get filled via SOES if the market tanks. If I price the order at the current inside price and the last MM leaves that price before I am filled, my order is cancelled and I have to enter a new one which puts me back in line whereas Market and Limit away orders will stay live in the SOES queue.
So occasionally, you see a vertical spread develop where maybe the bid is 50.00 at the inside, 49.98 at the next lower level, then 49.89 at the third level. Then the 50.00 bids print before my order is filled, the bidder at 49.98 cancels as he sees the stock selling, and then all of a sudden for just a second the market is bid 49.89 by a MM and my waiting SOES order is instantly executed at that price....just as more bidders come in and fill the vertical spread at 49.92 and 49.93 and 49.95 etc.
End result, market for the stock was for the most part really 49.9x by 49.9y while my order was live -except for a split second it hit 49.89 and SOES orders executed against it. Moral of the story, be careful with SS market orders in thinner stocks where vertical spreads are common.