This is a weird one. When you remove all magazines from the player and add it again, it will work for real magazines. But it will not work for smoke grenades. I really don't know whats up there :)
It is the same behavior for "addMagazine <STRING>" and "addMagazine <ARRAY>".
Spawning + uiSleep 1 after removeMagazines does not solve it.
player removeMagazines "30Rnd_556x45_Stanag";
player addMagazine ["30Rnd_556x45_Stanag", 1];
player removeMagazines "30Rnd_556x45_Stanag";
player addMagazine ["30Rnd_556x45_Stanag", 1];
// Player has one STANAG here
player removeMagazines "SmokeShellOrange";
player addMagazine ["SmokeShellOrange", 1];
player removeMagazines "SmokeShellOrange";
player addMagazine ["SmokeShellOrange", 1];
// Player has two smokes here