If you extend the flash, the ISO will not change from 100 even if you chose the most extremes of aperture and shutter speed as the flash is still powerful to lit the scene (as long as it is within the working distance of the flash). With the GF2, even if I set the aperture to f/16 and shutter speed to 1/160s in Manual Mode, the flash is powerful enough such that the ISO would still remain at 100. I am sure this is the same for the D90. From what you wrote, it sounded like the GF1 cannot do this.
It is only when the flash is not used that the ISO can have the chance to increase to compensate for the lack of exposure due to extreme aperture and shutter speed settings.
