This problem is back and the vehicle is broken. Once a greyhawk has landed it stops and cannot move again. Tested in vanilla on Altis.
EDIT: I just confirmed this problem is related to the land waypoint, if I manually engage the landing autopilot this issue will not happend

Confirmed, a lot of pbo's signed with the newest arma 3 tools fails with ".bisign is wrong. Err 0x20. Test FAILED!", pls fix this ASAP!

Confirmed, my RPT log is getting spamed with these, 19 errors a second!

Did some tests on this and it seems there has been some changes, there are now only 2 mags of 500Rnd_127x99_mag_Tracer_Red in slammer up commander turret (TurretPath:[0,0]) which actually means there is a workaround now:

When you empty a mag (or both mags) this will brake magazineTurretAmmo function as you said, but it reports all mags has a ammocount of 0, like this:
["500Rnd_127x99_mag_Tracer_Red:0","500Rnd_127x99_mag_Tracer_Red:0","SmokeLauncherMag:2"]

So when magazineTurretAmmo reports 0 rounds in all mags we know at least 1 full mag has been used, we can always get the ammo Count (and set it) of the current magazine with the ammo function (tank ammo "LMG_M200"), that way we can actually get all the info we need. However if there is more than 2 mags of the same magazine type this workaround wont Work, for example in the mortar, but there are very few vehicles that have more than 2 mags of same type in the same turretPath.

Im hearing the same thing from several mission creaters in the "Make arma not war contest", off the top of my head i remember missions like "Under the Eagle's Eye" and "Resist" mention this horrible bug on steam description, so its definitely happening. However i could not reproduce this bug, setting "this enableSimulation false;this hideObject true;" on a tanks init field and teleporting to the tank did not show any bugs, so a upload of a simple mission showing this bug is very much needed.

confirmed

Upvoted - we need what have been suggested here. I just did more tests, the original object reference is NOT objNull after the weapon is disassembled eg. _my50="B_HMG_01_F" createVehicle pos; The getPos on _my50 after it has been disassembled is a position on altis in the sea, so a workaround to get the reference to the weapon that was disassembled could be to check the cords against the sea pos, it should be safe as a weapon cannot be assembled in the sea, maybe that is why the sea cords was used? Anyway you can still get info on ammo and magazines on _my50 after its been disassembled. So _isDisassembled = surfaceIsWater (position _my50); used together with the EventHandler you can find out what weapon was just disassembled. Other info that could be useful is that if you do player moveInGunner _my50 (when disassembled) will put the 50 cal back where is was dismantled although bugged.

So this was supposed to be fixed since 2013 !? Its still not fixed, bad show..

I created a small addon that fixes the issues:
http://forums.bistudio.com/showthread.php?180909-High-Command-Transport

With the new fatigue system this is more important than ever, why is this not being looked into? It was reported more than 6 month ago?

Additional information i have found on the subject:
If you as player enter a vehicle (as driver) and then exit the vehicle, that vehicle will be blacklistet for any HC Group to enter it by waypoint, even if the vehicle is empty.

The fix:
I have fixed the issues by: assigning the units to the vehicle (eg. assignAsDriver) followed by the orderGetin command. This will solve all issues reported here, it is a relatively easy fix for a very annoying problem that currently makes the HC module less attractive to use, please fix this!

I thought i just throw this in here, maybe it will help someone, as it solved all my issues i had which was meantionen in this thread, putting my fps at a solid 60-70 on ultra settings in multiplayer with good CPU utilization (I7 quad core / gtx 970).

We all know arma 3 is CPU driven, my problem was my CPU cores was getting deprived of power! Win 8.1 and the manufacturers defaults power management plans (even on high-end desktops) to powersaving, my cores was only getting around 5 watts! I set the manufacturer power management software (asus) to high performance AND changed win 8.1 powermanagements to high performance, giving my CPU cores the 12-20 watts it needed to do the Work (jumped from 20-60 %) and watched my FPS settle between 60-70 fps on a 60 player filled server! Hope this helps someone.