I think I was wrong on ARP2 objects. Don't get me wrong, it caused major issues looking back on it with log spam and load times and unnecessary errors and probably wrong factions spawning and I don't regret removing it but I think the actual culprit was having 2 civilian placement modules as Highhead warned against.

I played for a couple hours(ish) on the server. Debug was off and everything was fine. This was just with removing ARP2 and JBAD when everything was ok (finally) after multiple tests. I decided BLUFOR may have been a bit too strong during my session so I went into the editor, changed BLUFOR spawn numbers and suddenly the issue came back. Debug on = more spawns again. And I tested this over and over after just removing ARP2 and I could not duplicate the error anymore but the problem suddenly came back again tonight.

Removed all but one of my civilian placement modules and now the issue seems to have gone away again. ALiVE is more of a delicate flower than I had originally assumed. It's crazy how problem was 'gone' gone and suddenly came back and then went away again.