Appears to be a problem with ammo simulation.
It looks like ammo with shotBullet uses weapon initSpeed, while shotShell and others ignore weapon initSpeed.

Video showing reproduction:
https://www.youtube.com/watch?v=2ubsR0dnlAc

No mods. The issue is easily confirmed by just looking at the config browser for the GMG weapon.

You can also reproduce by putting down a static GMG and add the following code to its init line:

this addEventHandler ["Fired", {hintSilent format ["Muzzle velocity: %1 m/s", vectorMagnitude velocity (_this select 6)]}];

Everyone can adjust the stance with the four (Adjust Up/Down/Left/Right) keybinds.
The problem was and still is that the Adjust Stance *modifier* key (modifier+WASD) was removed.

Okay this works now.
I don't know when it happened, but I can use any button as a modifier now, including mouse buttons.
For example binding Mouse5+W for Adjust Up works.

This probably worked earlier when Adam said it did, but it wasn't really apparent I could do it this way now.

Confirmed with the 1.42 update. The old bind is still in my name.arma3profile file, but doesn't work in game.

Created and tested with a new profile.
Stance modifier bind is not present in profile.

I tried adding keyAdjust[]={65540}; in my arma3profile file, which is my mouse5 button, but it did not work. This is the part that was broken in the Marksmen patch.

Unlike keyboard keys, you cannot use a mouse button as a modifier for a keybind, so binding the four new actions to Mouse5+W/A/S/D is impossible.

"Your picture has the barrel pointing up. You don't zero a rifle by lobbing a bullet. You aim it straight ahead, at a 90 degree angle. The bullet only drops, it does not go up; it does not arc."
Do you even know what an arc is? More to the point, do you even realize that when you're aiming a rifle "straight ahead, at a 90 degree angle", the barrel's actually pointing up a bit? That's how zeroing works. It's more exaggerated in the drawing to demonstrate a point, but it doesn't look like you understood that, either.

Here let me draw you another picture of what would happen if you did what you're suggesting. See how the bullet's not anywhere near where you'd be aiming?
https://dl.dropboxusercontent.com/u/66038154/UO/Pictures/Gunzeroing2.jpg

"If you are zeroed for three hundred yards and you put your point of aim (a chevron is the shape of the reticle) on someone high chest at 100 yards, it will go over their head."
No it won't. We're shooting rifles, here, not high-angle howitzers. Have you even tried this?

"PS - This is a definition of the word esoteric: known about or understood by few people. known about or understood by very few people."
I know the definition. In this case those very few people include everyone who's ever taken a high school physics course, but apparently doesn't include you.

Here let me draw you a picture. (It's not a pretty picture, mind, but you seem impervious to words). Note that the scope is comically out of scale for demonstration purposes.
https://dl.dropboxusercontent.com/u/66038154/UO/Pictures/Gunzeroing.jpg

Now to what you said.
"Only a muzzle pointed above 180 degrees would result in an arc."
Gravity and air resistance says you're wrong.

"My point here is that I shouldn't have the lower an optic to score a hit, with or without magnification. 200 meters is way too far for a Eotech or even an Aimpoint (red dot)."
See the picture for why this is wrong.

"If you put the tip of the chevron high chest at guy 100 meters away, you will send the bullet over their head."
Not sure what you mean by tip of the chevron, but if I aim the dot of the MRCO ("zeroed" at 300m) at the chest of someone at 100m, I'll hit their chest.

"It probably is that the reading on the screen is off and not the sight (or at least that is the way it seems recently), but they should both be correct."
They're both correct. See the picture for why it's so.

"FYI for those interested in this esoteric discussion:"
It's only esoteric for people who don't understand what gravity and air resistance does to a bullet's flight path.

"Assault rifles are always zeroed to 100 meters (or less)"

This is patently false. My AG3 was always set to 300m instead of 100, 200, or 400 metres.
Weirdly, that made the sight dead on at a range of 30m. That's exactly where your (unsourced, btw) average range is. Weird, right?

Besides, have you checked that the Holo sights are actually zeroed at 200m? Even if that's what it says in the corner of your screen doesn't mean that the primary aim point in the sight is at that distance.

And this ticket has no mention of calibre, weapon, or any other consideration.

If you look closely, you'll see the SW's magazine is a quad stack design with higher capacity than the regular magazines.

Compare: http://4.bp.blogspot.com/_mKgww2ohcsM/TPncAXWn5-I/AAAAAAAAAPk/DYYrnqbNa-g/s1600/surefire100rd.jpg

I have noticed that items seem to disappear from your inventory, but are still carried by your character.
Grenades in particular, which will show up in the HUD as Grenade x0, but you can still throw it.

The MX series and opfor rifles fire caseless ammunition, which do not eject casings.