The weapon mounted in the third compartment is not visible when arranging the warehouse.
have the same issue, hope they fix it soon, it was present before patch 2 
the first time i saw that i jumped on my seat, i had a legendary GS on this slot lmao …
there is a similar post somewhere about item slots being lock in vendor menus.
found it: Third weapon slot does not show in menus
here is another post regarding this issue: [bug] when browsing chests, main/off-hand enabled 3rd slot is locked