Here is the MDAT for the stacked sub measurements. Not sure where the 12hz hump has appeared from unless its been caused by physically placing one sub on the other. Probably shouldn't complain though at 12hz!It would be interesting to see if measured impulse response of your two sub configurations corroborates the subjective timing issue.
Looking at the REW room simulator I think that I should probably have tried inverting the sub where it was placed to the left rear of my sofa so I'll have to try that in due course.
I have included measurements of the centre and the combined subs from the centre channel as the centre is on a higher crossover lest you want to look at the timing of that.
Let me know what you conclude!