If Audyssey is off and you still have the issue.. not sure what it could be. Audyssey on, could be a poorly calibrated mic or a bad Audyssey measurement. If Audyssey measurements are showing low treble relative to your target curve, it will boost the treble when it shouldn’t. This is something that should be able to be figured out with REW and measurements to see what is going on.
Are you using the Audyssey app? If not, it is the best purchase you can make. Simply limit correction to somewhere around 200-500hz.
I thought about suggesting him to use REW to help investigating the cause too. Incidentally, I did use REW to compare the X3400H and the separates, based on FR and other plots I also saw no evidence of the X3400H doing anything funny that could add sibilance. On FR, the two curves almost overlap to the point with 1/12 smoothing they look like one curve.
I found the following article that seemed to support your idea that it might something to do with how the OP did his Audyssey measurements but then again as you also said if that's the case then the issue should be there only when Audyssey is on.
The spoken word is recorded in the most accurate way possible. Ironically, certain sounds we produce like sibilance can make recording very difficult. Why?