I just encountered this bug for the first time the other day and it royally peeved me off. Being clever though I got to working on why it was happening, so I ended up finding a solution.

When a weapon falls off a plaque or rack either in a vanilla house or a house mod, it has nothing to do with the plaque or rack but the unique ID of that particular instance of the weapon in-game.

So I had an Ebony Blade, a Ghostblade and a Keening that refused to stick to plaques. I tucked those 3 in a spare storage trunk, used the console to add them back into my inventory and voila! The freshly player.additemed versions stuck to the plaques just fine!
Obviously its not a fix, just a workaround, but hopefully it will solve some folks' headaches.

Kewl.
That's been an annoyance for me as well. I've only had it happen in Honeyside, but it sure makes it difficult keeping things organized.....