There are tons of threads on this, and it sounds like you are putting your "crate script" outside of the actual mission directory itself.... maybe somewhere else in /arma.
Try this script, I put a lot of comments at the top of the script making it super-easy.
Once you get my crate working, edit this script to add/remove weapons and the ammo inside it to suite your specific mission needs.
; Instructions:
;
; 1. Inside of your mission directory, make a subdirectory called "reload" and put this
; script in it called "ammobox_1.sqs"
;
; 2. Make a crate in the game
;
; 3. Put this as it's NAME: ammo_1
;
; 4. Put this in the item's INIT field: [ammo_1] exec "reload\ammobox_1.sqs
;
; Increment the ammobox tag for each individual box after this first one to load others
; IE: [ammo_2]... [ammo_5]...
; NOTE - This is my USA GUNS crate
; Get the crate parameter given
_crate = _this Select 0
; REMOVE STOCK ITEMS FROM THE CRATE:
ClearMagazineCargo _crate
ClearWeaponCargo _crate
; ADD THE ITEMS TO THE CRATE:
; West Weapons
_crate addweaponcargo ["M9",100]
_crate addweaponcargo ["M9SD",100]
_crate addweaponcargo ["M16A2",100]
_crate addweaponcargo ["M16A2GL",100]
_crate addweaponcargo ["M4",100]
_crate addweaponcargo ["M4A1SD",100]
_crate addweaponcargo ["M4GL",100]
_crate addweaponcargo ["M4A1",100]
_crate addweaponcargo ["M4A1GL",100]
_crate addweaponcargo ["M4AIM",100]
_crate addweaponcargo ["M4SPR",100]
_crate addweaponcargo ["G36a",100]
_crate addweaponcargo ["g36c",100]
_crate addweaponcargo ["g36k",100]
_crate addweaponcargo ["m24",100]
_crate addweaponcargo ["mp5A5",100]
_crate addweaponcargo ["MP5SD",100]
_crate addweaponcargo ["M240",100]
_crate addweaponcargo ["M249",100]
_crate addweaponcargo ["M107",100]
_crate addmagazinecargo ["10Rnd_127x99_m107",100]
_crate addweaponcargo ["Laserdesignator",200]
_crate addweaponcargo ["Binocular",200]
_crate addweaponcargo ["NVGoggles",100]
_crate addmagazinecargo ["30Rnd_9x19_MP5",900]
_crate addmagazinecargo ["30Rnd_9x19_MP5SD",900]
_crate addmagazinecargo ["15Rnd_9x19_M9",900]
_crate addmagazinecargo ["15Rnd_9x19_M9SD",900]
_crate addmagazinecargo ["30Rnd_556x45_Stanag",900]
_crate addmagazinecargo ["30Rnd_556x45_G36",900]
_crate addmagazinecargo ["200Rnd_556x45_M249",900]
_crate addmagazinecargo ["5Rnd_762x51_M24",900]
_crate addmagazinecargo ["100Rnd_762x51_M240",900]
_crate addmagazinecargo ["1Rnd_HE_M203",900]
_crate addmagazinecargo ["Laserbatteries",900]
; East Weapons
_crate addweaponcargo ["PK",100]
_crate addmagazinecargo ["100Rnd_762x54_PK"]
_crate addweaponcargo ["SVD",100]
_crate addmagazinecargo ["10Rnd_762x54_SVD"]
Exit