You have to Understand that Followers are definitely better used in Real Time, I mean sure, TB is somwhat necessary at first levels, but the real advantage to NPC followers is 1. you will die WAY less often. 2. You will win way more often (if your smart). and 3. You have something to do with all the caps you will eventually accumulate.... 4. Followers use their aps immediatey and more efficiently, and can aim in real time INSTANTLY, so if you hve 5 sniper mercs, you could quite literally destroy ANYONE 1vs1, or... 1 vs 6...

, And its really really fun.
Your problem is "possibly" your giving commands to them when they're out of your sight, they have to be within your FoV for your command to get through, other wise you must've put them on kill all npcs, which, upon the npc leaving the slave/merc's FoV, and reentering as it looks back toward the area, the NPC will be considered hostile once again.
Btw, Friends means Friends of a faction base. Not who you tag green, but that would be pretty cool.