Thank you guys for the help.
I already figured it out what is the problem. Is related to the Aperture ring coupling of the F100.
Basically when the lens is mounted and I set the aperture ring to, for instance, f16, and I move back to f2.8 this plastic aperture ring doesn’t follow the aperture ring of the lens. That was why that the camera was giving stupid different values of the shutter, because I though that the aperture was at f2.8, but in fact the the plastic ring of the F100 was at f16.
I forced the position of this plastic tip with a piece of paper and I set it to the correct f2.8 position, and after that the meter reading was matching with the one with the AF lens.
If there is no lens mounted, the ring moves freely, and seems to be ok. But when I mount the lens, gets stiff, and don't work properly.
Do anybody know if this is a easy fix? I could send it to the Nikon repair service, but I am afraid that they will charge me more for what I paid for the camera.
Well, at least now I know what is the problem now, it was driving me crazy.