50 on the 1ds is a tad cleaner that 100, but you do lose considerable dynamic range. You will see this in shadows more than highlights, at least with my camera.
Most times I use 100, but like the previous poster, sometimes will go to 50 in place of a ND filter.
No sure why anyone would be getting more noise in the lower ISO's on a 1ds, or any camera for that matter as the lower the ISO, the less noise, thats a general rule.
Paul Caldwell