Problem/Bug Annoying glitch =/

Theres this really annoying and game breaking bug where whenever i break a block the id of that item reverts to 0, example: i break a block with grey stained glass it turns back to white, i use my pick, it gets fixed.
please help these are my plugins:
RealMOTD, WorldEdit, Essentials, EssentialsProtect, EssentialsChat, ClearLag, PermissionsEx, mcMMO, SpawnJoin, RandomTP, Vault, EssentualsSpawn, MassiveCore, ProtocolLib, WorldGuard, LibsDisguises, Factions, RandomLocation, SignShop, WarpPortals, SilkSpawners and iControlU

plz help because this is annoying when building stuff (and game breaking)
[Edit: i tested with defualt rank in PermEx and it still does it]

 

i realised i didnt properly explain,
if im holding an item with a damage of 1+ and break a block the damage of the item im holding reverts to 0

 

Take a look at the video below, it'll show you how to troubleshoot your plugins which will allow you to figure out which plugin is causing the problem (provided it isn't a vanilla glitch, which I doubt):