You may want to go through and check all settings... I normally use the optical finder only, so I don't really notice this.
One thing I have experienced when using ND Graduated filters is "exposure shift". With the camera set to full manual mode, including fixed ISO, the exposure of the shadow area changes as I alter the strength and location of the ND Grads... my only 'guess' is the Dynamic Range setting (??) -or- because I shoot only in-camera JPG. The documentation is poor...
I really like the X100T and will not give it up ; )
Canon 5DII, 35 f/1.4L, 85 f/1.2L & 70-200 f/4L
IIIf, Canon 28 f/2.8, 50 f/1.8, & 135 f/3.5
MP, 28 f/2.8 ASPH & 50 f/1.4 ASPH plus CV15 f/4.5
Nikon F3HP, AI'ed Nikkor-H 28 f/3.5, & Nikkor-P 10.5cm f/2.5
Nikon F3P, AI-S 20 f/2.8, 35 f/1.4, 50 f1.2, & 85 f/1.4
Fuji X100T, 23mm f/2 fixed lens
Mamiya RB67, K/L 90 f/3.5 L
Nikon Coolscan V ED & Epson GT-X830