If the 100mV and 1V ranges are affected only, but not the 10V range, then it has nothing to do with the references, but with the x10, x100 DC amplifiers, or the signal path including the jacks in front of the amplifiers.
I'm also no fan of the fan, especially inside the 3458A, where the air is also blowing across the LTZ1000A circuits solder joints, which is NOT recommended by LT.
Same goes for the reference of the 34470A, only the solder joints of the LTZ itself are protected.
Maybe I'll do some experiments with my 3458A.
Frank