I posted this at the nexus forums with no luck. Maybe somebody here can help me..

Hey so, first of all I'm talking about any MOD added companion, whether through NCSS, RRVault or any other method.

When I "fire" a companion they go into sandbox mode, but they still act as if they are following me. If I pull out my gun, every companion in sandbox mode pulls out their weapons too, and puts them away when I do. This will indefinately cause a crash with too many companions in the area. What really annoys me, is that I used to be able to get them to take out their weapons, go into sandbox mode totting their gun around and would almost never put it away.. I would have patrols, and armored bases, now my entire experience is compromised!

At the moment this seems unfixable to me, because I have deleted my entire Steam directory and My Games directory everytime after re-installation. It seems to me like there is a type of cookie on my computer somewheres that remains after re-installation. It doesn't matter what companion I have, or what system I'm using. Is there anything in the ini files that will fix this?
I am going to try one more time and then I'm pretty much SOL, unless somebody helps me out.
Any solutions or suggestions are appreciated!

Did you re patch it?

I thought steam automatically detects for patches.
In New Vegas directory my files say version 1.2.0... etc.

I also have NVSE 1.0.6 beta if that helps.

Are you using that mod that makes companions pull out their weapons when you do?
Since you specify mod added companions, my guess would be mod conflicts and a load order that has somehow become different since you reinstalled.

Try unchecking all mods, one at a time?

Man.. this is so weird.
No I don't use that specific MOD. I have my vanilla companions pull out when they want.
If your talking about a MOD that makes all non-vanilla companions pull out their weapons and keep them out, please point me in this direction!
Yeah I would expect this to be a MOD problem, or maybe even something with FOMM.. But everytime I'm done reinstalling I try different companion MODS. First I tried NCSS only, then I tried RR Vault only I also tried Shojo companions only. The same result each time!!
Thanks for that suggestion, I tried that too.

UPDATE: If I go into console commands and type in setalert 1 to any NPC they will take out their weapons. If I type that in to one of my following companions they will not draw their weapons unless i do, insinuating that they are already in alert mode. Doesn't that sound like something to do with the ini files?