If its consistently 5 seconds I would think you could diagnose it.
I do a check for the war status every 60 seconds so it's probably not that Could be the check intel script. Look in pulse.sqf and that should show you all the cyclical checks.
Since you are running your own version you could remove the version check which may run every 5 seconds since its worthless to you? Just some ideas
Sorry but I don't notice any consistent hiccup like you describe