I bought my marlin in 44 mag about 5 months ago mainly to use fer deer hunting. I have been shooting it a few times, just messing around and not fer accuracy. I did notice it was shooting low those times as well and didnt mess with the sights all that much since it was all offhand shooting. Yesterday, i decided to shoot some groups. I was shooting prone with a sling. The groupings were pretty good, however at 40 yards i had the rear sight all the way down and was shooting between 4-5" low. I was also shooting 44 spl since its quite a bit cheaper. I threw in a few magnum rounds to see if that had any effect (which it didnt). Is this normal lr are the sights off, or possible a problem with the barrel? This is my first lever gun, so i am not sure what to expect from it. I already planned on replacing the sights and going with a scout rail and either rds or low powered scope.

You raise the rear sight to raise POI. 

Get a shorter front sight if you have run out of elevation on the rear sight.

Need to raise the rear sight or get a lower front sight to raise the impact point.  You need to move your rear sight in the direction you want the bullet to move.

Raise the rear!!!!! If still a no go then a shorter front is in order

What weight bullet are you using?  What is the velocity?  Compare those to what the factory uses to sight in and you may find part of the reason.  Also, different folks will have different points of impact with the same rifle and ammo.  So, decide what bullet weight and velocity you want to use, sight in for it and go hunting.

Yes... This... Remington has been known to install sights that are too tall making the rifle shoot low.

Has any one mentioned you moved the sight the wrong direction yet?

????? That's interesting.  All the Special and Cowboy loads I've seen have been the same price as Magnums.

Well i guess i am the dumba$$. I was figuring that moving it down would in turn raise the front and the poi. Yeah, around here i can get a box of 50, 44 special for around $35. As where the 44 mag is $55 for the same amount.