As Rob says, there is a question mark against the frequency response of your speakers, and another against the frequency response of your mic.
Without knowing how good those are, measurements are pretty meaningless.
I took a look at the GIK help pages:
Their explanation of a waterfall plot is complicated.
They say they use a stepped sine sweep, but then the explanation says the waterfall plot is created from the impulse response.
Is it an impulse or a sine sweep, can they make their mind up?
Then they talk about 'convolving' a filter shape against the impulse response (in the time domain).
I'm getting tied in knots trying to understand their explanation.
If I can't grasp what they're getting at, what hope have you got, CharlotLouie?
Take a look at the link above, and see if you can follow it.