Because with flash, auto is relative. It's not going to leave your aperture and shutter constant, and then do ISO adjustments. If you shoot in Av mode for instance, it will change shutter speed, relative to your aperture already chosen by you, and the ISO the camera chose. Change ISO to something else manually, after the camera already has chosen your shutter speed, or another way is shoot manual on the camera and ETTL on the flash.
In manual, this isn't an issue. You set everything. My recommendation is that you do not use auto ISO anyways, since afterall, metering is sort of relative too.