I got my ammo crates to work again... Go the the server.pbo system folder and the server_cleanup.fsm and comment out the following code:
"//Check for Ammobox" \n
"// {" \n
"//if(!(_x isKindOf ""WeaponHolder"")) then {" \n
"//diag_log (""CLEANUP: DELETING AN AMMOBOX "" + (typeOf _x));" \n
"//deleteVehicle _x;" \n
"//};" \n
"//} forEach allMissionObjects ""ReammoBox"";" \n
"//*/" \n
""// \n
"//Check for Ammobox" \n
"// {" \n
"//if(!(_x isKindOf ""WeaponHolder"")) then {" \n
"//diag_log (""CLEANUP: DELETING AN AMMOBOX "" + (typeOf _x));" \n
"//deleteVehicle _x;" \n
"//};" \n
"//} forEach allMissionObjects ""ReammoBox"";" \n
"//*/" \n
""// \n