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Flip up sights are what they are - back up rudimentary aiming devices. The best you'll do with them off the bench at 100 is gonna typically be around 4~5 inches. If you can hit a man in the chest at 200 they are working as advertised.
Sounds to me like something is moving around. I would have a proven shooter take a swing at it, and if he gets the same results and can't help you out... Then it's one for the smith.
If I had to guess it would be the ammo that's the issue not the iron sights.
I put some of the federal 149gr fmj ammo through my remington 700. It would hold zero for a rounder or two then i would get a random round up to 3" away. It was incredibly frustrating.
With 168smk's reloads it does .75" at 100 with 5 shot groups.
Try a box a FGGM 168gr through it and see what happens
Is your gas block pinned onto the barrel with taper pins, or set screws? If the gas block moved, and then you moved it back, one of a number of things may have happened. how did you move the gas block back into its original position?
Check that the gas key is not binding with the gas tube.
Take the bolt out of the bolt carrier group and run the carrier into your upper - there should be no binding of the carrier with the gas tube. If there is, this can affect accuracy and give you some inconsistent results.
Having said that, it may well be your ammo / rifle combo. Shoot 10 round groups for your mpi and adjust your irons accordingly.
The block is held in place with set screws. I just put it back to where I imagine is the correct position on the barrel and tightened it back on with the screws. Gas tube was not bent, the block its self seems to been fine as-well. BCG isn't binding. I understand going to heavier, higher quality ammo will increase the accuracy I'm just being cheap I suppose. I still felt I should be getting better groups at such a relatively short distance. Maybe it is a mix of over estimation of iron sight capabilities, not the best ammo choice and some bad posturing by self
Thanks for the input, I will make sure everything is looks right, use some fancier munitions and take my time with the shots. See if I can tighten it up a bit.