See the bugs listed on this [wiki page][rack]. Apparently weapons can fall down, disappear, move etc using weapon racks.

Even a bigger problem, the staff of magus is a [known bugged][bug] item on weapon racks.

If you are playing on the pc, there are some dodgy [solutions][sol], but they focus more on weapon racks that are not usable, not the disappearing weapons.

You could use the no clipping mode. (open console '~', type in 'tcl' close console). And walk through the walls to look for it.

Or you could spawn a new staff of magus using a console command. In the console type in 'player.additem ITEM "00035369"'. You should have a new staff of magus in your inventory. ([00035369][item] is the item code for the staff)



 [rack]:http://elderscrolls.wikia.com/wiki/Weapon_Rack
 [sol]:http://forums.nexusmods.com/index.php?/topic/724230-dysfunctional-weapon-plaques-and-racks/
 [bug]: http://www.uesp.net/wiki/Skyrim_talk:Staff_of_Magnus#.22Sinking.22_on_weapon_racks
 [item]: http://www.uesp.net/wiki/Skyrim:Staff_of_Magnus