My test roll E6 was shot on all 36 exp's in matrix metering, subsequently 12 series of A, P and M modes. Each P frame(total of 12) came out underexposed. All 24 A and M frames were OK.
I used all true nikon lenses(I own only 1 sigma 105mmf2.8): the first 23 frames a 28-80 f3.5-5.6 AFD zoom and all the rest a 75-300 f4.5-5.6 AF to rule out if this D thing is of any influence in P/S mode.
I checked P and S mode again in spot and matrix: dark subjects yield in opening aperture almost completely(f4,F3,5), very light subjects and same shutter speed dailed in yields in smaller aperture(F11,F16,f22), my conclusion is here: the camera is stopping down correctly.
Leaves the big differences in shutter speeds when compared to the F100 - all were almost half, thus underexposing a lot .The F100 is a trusty machine, never had any troubles with it.
So the shutter operation in S and P is not correct and needs checking or replacing I assume.
Any further thoughts from your side?