HELP: Suddenly all factions in Chaper 2 give me alerts

[Ivotas]

Hey guys, hope somebody can help me here. I'm currently on my Big Boss Emblem playthrough and I made it to chapter 2 safe and sound. I'm in the very first stage of chapter 2 where the PMCs and the militia start fighting each other. Actually I got even past this part but didn't save so on the next part I get an alert phase. No one else to blame but my I guess so I reload the safe file and do the same thing I just did before. Only now even the militia is my enemy. So even if I take out all the PMCs and move on as I did previously (and as Vashs video guide suggests) I constantly get an alert phase by the faction that were my allies in the previous attempts.

 

This makes going on with the playthrough pretty much impossible because now I have to avoid NPCs I should actually be running amongst. So my question is if there's any way to fix this? I even deleted the save files and started all over from the briefing with the same result. All the militia have red letters written over them when I look at them in night vision mode. Previously it was green. Is this a glitch?

 

I really hope somebody can help me out with some info here. If I mess things up I have no problem fixing my approach but if this is a game breaking bug it would truly suck. =/