Can we get some specifics?  What range is this 2nd position?  What is your experiance/training with a rifle - cause it sounds like shooter error ?

This is not an uncommon issue.

First some facts:
1) With an Aimpoint at 50y it does not matter where the dot is in the display (nose-to-charging handle is not required).  If you can see the dot and put it on target it will hit where it's supposed to.

2) You can never have a 5.56 round hitting 30" high when you've zeroed correctly (4moa or smaller groups at a standard zeroing distance), and when you're correctly applying basic marksmanship techniques.

So it's not a mechanical issue (unless your barrel can wiggle in the upper receiver).

I'd check the following:
1) Breath controll - poor breath control can have you shooting very high.
2) Change in tension on the barrel.  Things like using a tight sling, resting the end of the barrel on sandbags etc. can cause changes in impact - particularly if you have the tension in one shooting position but not the other.
3) Flinching

For these kind of issues you need to be under the eye of a shooting coach/trainer (or at very least a very experienced shooter).