I've had simular problems with SIM3 while working on phase correcting a line array system build in the netherlands . Working with SIM gives you the possibility of looking at the processor phase and frequency response without having to repatch things .
It took me a while to figure out to get the real response of the processor within SIM because if i synchronize it the processor also gets synchronized (find delay auto small or what ever it's called within the software you use) .
Because i'm working a lot with all-pass filters i wanted to see what the processor was doing without all kinds of delay settings messing up the view of what these filters do .
So because i had to start from scratch i took a full-range trace without filters what so ever of each driver (at very low level in order not to burn up the drivers and to find the best points for the x-overs) .
Within SIM you have to program branches where you tell the machine measure this processor channel/speaker with this mic (out of six in my case) .
The last time i programed each branch and then dubbeled them so i could allways go back to the point where i only measured the latency of the processor itself and not a trace that's influenced by group delay caused by different filters . This allows me to get a view of what filters do if i do not synchronize after that (on the branch i double at the start of the measurement).
To do this with the BSS units and your software you might want to take a measurement of a output with no delay's or filters aplied so you only measure the latency of the processor it self and store the delay value (probably about 1.5 to 2ms).
After that take a processed output and measure it at the time you got for the processor latency .
http://timobeckmangeluid.wordpress.com/2012/05/03/alignment-the-x-over-point-using-2nd-order-all-pass-filters/ I think this is the link to the first part of that measurement (not sure and i have no time to check that at this moment)
Hope this helps.....
By the way i already tought it was a notch but it has been a while since i worked with NTM filters when i ways practicing with reading the phase display and training myself to see delay time values without having to think about it (not a chance in my case:-). Couldn't remember how the response was on them but it looked a bit like the NTM .