I am having the exact same issue since yesterday's update. Trying to get mine to save right now.
I posted an RPT and alive plugin log in another thread, but here they are again...
https://www.dropbox.com/s/27qguvtt51vpor6/arma3server_2016-04-13_16-10-18.rpt?dl=0
https://www.dropbox.com/s/dskaubda7v29rpf/aliveplugin_2016-04-14_07-56.txt?dl=0
Weird.. it's working now. I closed my server down, and uploaded a new version of my map with a couple of tweaks, and re-uploaded the new version of Alive to the server. Even though I had updated to 1.03 earlier today, when I join the server it tells me that the server is still on 1.02.
I double checked that both versions are the same, even copying the files from the server to my system, and it still tells me they are different.
Meh, it's saving now...