Does this happen for JIP players and not players who were on the server at the moment of "setVariable" use?

You could try if EntityCreated eventhandler is triggered when a building is streamed in.
That way you could set the var when the building re-appears

In T170985#2419216, @SaMatra wrote:

Does this happen for JIP players and not players who were on the server at the moment of "setVariable" use?

In my case all the variables are set when the server starts so there is nobody on the server.
When players join, every building are locked for them.
And then 1 or 2 hours later, some players (very few, like 5/100+) randomly don't have any variable set on some buildings (not all) anymore.

In T170985#2419635, @dedmen wrote:

You could try if EntityCreated eventhandler is triggered when a building is streamed in.
That way you could set the var when the building re-appears

I will try to log this event

Please let us know how it went, I had similar issues with streaming objects, yet to make a repro and ticket so I'm very interested in your case.

So i've put a log on EntityCreated and BuildingChanged events, none of these have logged the "bugged" buildings.

I guess i will solve my problem by reconfiguring every userActions of the buildings, to use a custom script in the statement instead of BIS_fnc_door, which will check a hashmap that every player has locally instead of the bis_disabled_door variable.
The map will contain the netID of buildings as key and an array of locked doors as value
But this solution can only work on modded servers, and is a lot of work for a problem like that.

I recently had an issue where buildings failed to receive scripted (HandleDamage-returned) damage for JIP players. I chose some building far from the action, damaged it, restarted the game, rejoined and it had wrong damage numbers. My guess was that game mixes up which entity should get which damages, maybe it does it the same with variables. It was pretty reproducible last time I observed it, I'll make a ticket some time.

Out of curiosity, join your server after its well into the game with fresh Arma 3 start, then check ALL entities on the map and see if it has bis_disabled_door_1 on it? Maybe some fences or unrelated buildings got the variables instead of intended buildings? Maybe record number of buildings that should have this variable on them normally VS how much you'll get as JIP well into the round.

private _objs = nearestObjects [[worldSize/2,worldSize,2],[],worldSize*2] select {!isNil{_x getVariable "bis_disabled_door_1"}};
diag_log ["count _objs", count _objs];
{
	diag_log [typeOf _x, getPosWorld _x];
} forEach _objs;