That sounds exactly like the problem I'm having on my server. I've been trying to run MArtials Takistan NATOFOR ALiVE mission in it's most recent form, as well as modified versions to fit my unit's play style, and this is happening to me.
I can run the server, it will populate with units as normal.
I can join, others can join, an we can play with player or ALiVE generated missions. But at some random point ,2 minutes in or 2 hours in, it will freeze up for one or more players. It will not crash, just freeze things in place while one or others can still move about.
We have to ALT+F4 out, or if possible exit Arma, and try to come back in. Server will show as up, but we cannot load back in.
Most recent RPTs I have for it I think:
https://www.dropbox.com/s/ayzs4i6tlcnpt89/arma3server_2016-01-22_04-24-45.rpt?dl=0
https://www.dropbox.com/s/efxmsxdoaoxxqxi/arma3server_2016-01-22_00-53-34.rpt?dl=0
I will try to remove the C2ISTAR module and see if only running it with Player generated missions will fix the problem.
Edit:
Just loaded up my version of NATOFOR (just tweaked medical and TFAR a little, changed bad guys to ISTS) with the removal of C2ISTAR. So, autogeneration of tasks is gone like I expected, but it also removes manually generated missions completely. So, there are no tasks that are able to be generated.
I see that OpFor units are still being placed by ALiVE OpCOm, so I assume the Mission just becomes Sandbox at that point , with players tasking missions for themselves, or Zeus placing missions.
@ Monty, Would that be a fair assessment of what you guys are experiencing?