Hi Jens. FM is a typical Mac program. We do not get to see under the bonnet.
There is no access to the underlying FFT settings.
The only obvious settings available would be length of sweep. (I recommend 10S rather than the default 1000mS) and the Window length, which also gets set automatically, but generally works fine.
Here's the same measurement I showed a while ago, but at 1/48.
One way or the other, this looks like a measurement which needs to be redone, at a higher level, one speaker etc. etc.
Carc, you can Export Impulse Response, Zip it, and post directly here. Then anyone can Import into their own software to view in any form they wish.