Just to add to the comments already given, distortion will also lower coherence.
So if you are overdriving part of the signal chain, that could cause the problem as well.
Is your delay time set correctly? Does it make sense to what your eyes say?
Reflections are one of the hardest things to understand when taking measurements. Is that something I can EQ, or is it a "local problem" due to a reflection.
The phase trace along with the amplitude will give you an idea if you should attempt to eq it, or will it make it worse for other people while "appearing" to make it better for one location.
A general rule is that if you have a dip in the response, and that freq is also in the middle of a small phase shift, just leave it alone, there is nothing you can do about it in reality. But it can "appear" to improve on your screen, depending on the amount of smoothing you are using.
