Okay, so, as an update, I removed the ARs and it works fine now with the peg-less shells. Fires really well and has a nice "THUMP", even with normal (non-slug) darts.
I still don't really know for sure what was causing the issue, but after some testing I think I might have an idea.
I noticed that only the bottom (center) one would fire a good distance, EVEN IF there were no other darts in any other barrels. So, for example, I put a dart in one of the upper side-by-side slots, and they would fire like crap. Put one dart in the single bottom slot, and they would fire great. I tried rotating the shell, and still only the bottom single slot would fire correctly.
My theory is that after cutting the pegs out you end up with a bit of space where the AR can accidentally slide inside the rear of the dart, instead of being opened by the edge of the dart as it should. For whatever reason, even though the dead space is the same on each shell slot, the bottom AR has less "give" or something (less wiggle room for the AR peg to become misaligned) and that is why that one works. I did fiddle with pushing down the ARs a bit and it did seem that the top two had more "wiggle" than the bottom.
So with this theory it's entirely possible that, depending on your blaster, it may or may not work properly depending on the tolerance of the ARs.
If it's not that, then I seriously have no clue. It shouldn't actually matter either way if the ARs were designed properly to not wiggle around, but the center piece of the dart peg apparently keeps them stable whereas without that part, they can slip and not fire properly.
I haven't removed the AR yet on my Sledgefire, but one interesting (and kind of lame) thing I noticed is that after I removed the posts from one of the shells, the darts don't fire evenly out of that shell anymore. Which makes very little sense, since the posts don't hold down the AR pegs or anything, the dart itself does that. Basically what will happen, though, is that one dart will fire really far and the others will kind of just flop out about 5-10 feet in front of the gun. My only guess is that maybe removing the pegs somehow made the darts fire out less evenly, causing most of the air to go through one slot and not the others. However, this doesn't really make sense because I cut out each peg evenly and the darts are identical.
I assume doing an AR removal would solve this, but I'd kinda hate to lose the ability to fire less than 3 darts at once.