Make sure to look through the Data and Player Options modules and make sure everything you want saved is set appropriately. Read the wording carefully as some of them are written strangely IMO.

Also, go through each and every module and make sure persistence is set to yes.

My favorite way to confirm persistence is working is by either laying down an advanced marker before saving or even easier is just looking at the time in the map menu (make sure time is set to persist).

In the event you have everything set up right, post your server rpt back here for the Devs to look at.

I actually don't mind looking at your settings for you if you think that could be the reason if you want to share the mission (assuming it doesn't require a lot of mods I don't have).

EDIT: You have a War Room account with your server info, right?

If markers are saving I'd assume persistence is working. Though note, I have not tried persistence since 1.60.

Is time set to persist? It's set to no by default.

Is player position set to persist?

Are you logged in as admin (I'm assuming you are and I'm not even certain that matters. I always log in as admin and have never tried saving without it).

Ok a couple other things. I'm going to assume it's not the problem since no one has reported it but maybe the dev build of ALiVE will work (it fixes a specific error which in some instances can break ALiVE's initialization process though I fail to see how it could break persistence. Who knows!):

https://www.dropbox.com/s/w43u8v3dy7z8864/ALiVE_testVersion.zip?dl=0

Also, just shooting off the hip here, but if you're running your server on your same computer as the game, make sure alive.cfg is in your Arma root and also that @aliveserver is running on your server (I like to place it very last in my server load order).