Ever since Arma II (at least), this problem has been present: Usually mods are, if configured right and loaded properly, active as long as you play multiplayer or start a new single player mission. But as soon as you resume to a savegame, some mods are no longer active.
In most cases mods that have a key-combination to have their functions toggled (for example Strg+R for Outlaw's Mag Repack, or something else defined in a userconfig-file) or that are being toggled via the action menu, are no longer available in a resumed savegame, although they're being properly loaded and seem to be active in the main menu.
That way playing the single player campaign (for example) is not as much fun as it could be.

Additionally the mods are being written into the save game. Deactivating the mods renders it impossible to resume to the very same save game. So you have to have those mods activated although you can't use them. That's almost the most annyoing thing about this 'bug'.

Please make this a priority to fix, as this problem is not very modding-community-friendly.