JD - I believe your problem is not a problem at all. This is assuming you are shooting a scoped rifle. If you can envision this: your line of sight (scope) is looking at the bullseye at 50 yds. If you sight in to impact the target 2" high and your scope is 1 1/2" above centerline of bore (avg) your barrel is pointing relatively high. It is probably so high that the bullet is not coming down far enough to impact at point of aim at 100 yds.
I suggest you sight in to be 1" LOW at 50 yds. Then try shooting at 100. From there you can adjust your scope to be on at 100 and shoud be close at 50.