Ok, I did some more investigating as follows....
I setup 2 client machines and the server, selected MH-BaseRiot-fix on the server. One of the client machines I had join as a spectator, the other as a real player, I had the spectator join first and moved the viewpoint to just outside the base where there are a load of Skaarj lined up, and watched what happend when I joined on the other machine.
Initially the skaarj would just be scanning the area, with just the spectator connected. What happened when the real player connected depended on what mutators the server had active (I have MapVoteLA13, so can switch on the fly).
With just MH/UJMH the skaarj just stayed scanning until a player actually wondered into their line of sight, and then they attacked the player, of course they still fought if they happened to hit each other but most of the firing was directed at the player.
With some other mods (I tried using the insta mutator as that is something that would be easy for others to try), the skaarj again did nothing until the active player spawned and then they imediatly stop scanning and start hand to hand fighting each other, even before the active player has fired a shot.
As the other mutator that I am having this problem with is again a weapons replacement thing it might be someting to do with that.
Cheers.
Phill.