I've never seen that kind of variation in the convolution module myself. You say the measurements were taken with no changes between them; was the microphone in the exact same position? Have you tried using less or different smoothing to see if the raw data looks similar?
Nulls of that size are generally only caused by cancellation effects (two sound sources exactly out of phase). Examples of phenomenon that could cause that kind of cancellation: room nulls (caused by out of phase reflections hitting each other), two sound sources interacting with each other in a destructive way, or a misaligned crossover. For example, a well known phenomenon called "comb filtering" occurs when two speakers are playing at the same time, which creates a jagged looking measurement where the speakers cancel, don't cancel, cancel, don't cancel so it looks like a comb. And the interaction between the two will differ at different room positions based on how far the speakers are apart, what they're playing, etc. Pro audio is mastered with the effect in mind, but test signals are clearly not. This seems likely as you don't see it with the speakers playing by themselves, but do see it in a composite measurement. FWIW, I don't recommend that anyone measure all speakers at the same time for anything other than getting a sense of total volume levels for exactly these reasons.
Two theories:
1) If the microphone wasn't in the exact same spot, my guess would be that you may have inadvertantly moved it into an area of the room that had a different interaction with those frequency bands, or in which the speakers themselves were interacting differently. Room nulls or comb filtering can be very location dependent, the "anti-sweet spot" can be physically very small, and the roll off is very steep, so even moving the mic 6 inches or so can be enough to change things if you happen to land at the center of the null. If you're seeing these results a few minutes apart without touching the microphone, feel free to disregard.
2) Alternatively, smoothing can sometimes mask very narrow nulls, such that I've seen two measurements where the smoothed graphs looked pretty different, but the raw data looked fairly similar, it's just that one had a null that was slightly narrower than the other, if you see what I mean.
It's posible there's something wonky with the convolution, but I've never seen that myself in a few years of use. Maybe other convolution users can chime in too?
EDIT: I just saw in the update to your REW thread that you used REW to mathematically sum the individual speaker measurements as a test and got the same null. You're almost certainly seeing comb filtering or inter-speaker phase cancellation.