Actually, whether you have had auto execution orders stuck in SOES queue is quite relevant. If an auto ex order sees that the inside market is a market maker and attempts to place a SOES order, and the order gets in line behind other SOES orders, the 'smart' thing to do would be to keep scanning for ECNs to trade against, and cancel the SOES order if that happens. The fact that you have seen it get stuck in the SOES queue and not attempt to trade against ECNs confirms that it doesn't work the way I had expected that it would.
BTW, since you said that there's a guy who changes the order routing function for each broker...is it possible that some brokers offer the ability for auto ex to continue to search ECNs while it's in line to get a SOES order?