So I've run some tests since I started experiencing this bug a few weeks back, and it is a little odd, but bear with me.

It seems that when I deposit armor into anything but a mannequin, after a random amount of items the game just quits. No prompt, no crash log, nothing, just closes. This also happens with putting weapons into anything. I've been getting around this by saving, putting a few items into the container, backing out, saving, and doing it again. This is annoying, but not game breaking.

Now, I'm running the game HEAVILY modded, so that is probably the issue, but I'm not sure which mod it could be (I'm running about 50 mods, most of which are added armors and weapons, along with about 2 house mods. I can provide a list later, I'm currently at lunch at work.)

Any advice on this with what info I've currently provided?

Uninstall (do not simply disable things, their files need to be gone from the Skyrim directories) any and all mods, injectors, script extenders, 3rd party add-ons, etc and try a new game. If the issue goes away, then it's likely a mod issue and goes here: http://www.gamesas.com/forum/183-skyrim-mods/