I have never had the pleasure of trying to explain this in writing but sounds like a sight over bore issue. A bullet does not rise after it leaves the barrel. What makes it seems like it is rising is the fact that it crosses your line of sight through the scope at the zero distance. That is why ballistic programs like to know how high the center of your scope is to the center of the bore. It is done mostly at 100 yds as a standard because a 1/4 inch of movement at that distance is 1 click as you get closer it takes alot more clicks. That being said at 50 yd it would be 1/8 of an inch. At 20 yards being zero with a flat caliber and your scope is 1.5 inches over bore, at 40 yards makes you an 1.5 inches high. If your zeroed at 20 yards your next point of impact that will be dead on with no scope adjustment would be about 310 yards with a .243 standard 100 gr pill. If you zero at 100 your going to be less than .75 of an inch off at 25 yds and .25 off at 50.
This is of course assuming the gun and glass are functioning correctly!