Thing is when i restart the server stuff from backpacks disappear and i dont know why since its not a wipe. All permissions are gone then as well and I need to set everything again just bcoz server restarts. Any idea what can i do to prevent such thing?

posting your config might help people understand the problem

It may have something to do with how u have the config set to handle saves.

Well since im new to hosting servers and all those stuff Im not sure which config you want me to give pic heh
{
"Drop on Death (true/false)": true,
"Erase on Death (true/false)": false,
"Use Blacklist (true/false)": false,
"Clear Backpacks on Map-Wipe (true/false)": false,
"Only Save Backpacks on Server-Save (true/false)": false,
"Blacklisted Items (Item Shortnames)": [
"rocket.launcher",
"lmg.m249"
],
"Backpack Size (1-7 Rows)": 1
}

is it this one? or sth else

Is this happening to you every time you restart your server?

hello, this is happening everytime the server restarts.

Ubuntu server 

Sorry for the delayed response; I wasn't able to reproduce this in my testing. Additionally since you described you're loosing granted permissions, this sounds like a more general problem you're having since Backpacks is not managing permissions.