Whenever I spawn into my map, 4 out of my 6 mystery boxes are glitched. One is properly starting with the box in place, the other properly spawns with the teddy in place. And then the other 4 spawn with the box and teddy together. I've tried using different kvps, tried removing some of the boxes, nothing works for me! If someone could walk me through fixing it, that would be appreciated! Thank you!

KVP's aren't correct.

Make sure your boxes are numbered 0 to 10. Select box that doesn't work and determine which number it should be, rightclick>enter prefab.
Move the camera inside the clip, right click on the struct >select "script_stuct"
under script_noteworthy the value should be: chest_# (ex. chest_1)

Now right click on the struct> select "zbarrier_zmcore_MagicBox"
This is where I messed up when editting the box:
under script_noteworthy make sure the value is: "chest_#_zbarrier" (ex. chest_1_zbarrier)

I mistakenly copied "chest_1" and pasted it into the other struct which is not correct as the two values are not identical.
The first one is just chest_# and the other is chest_#_zbarrier.

I used this tutorial:
http://www.youtube.com/watch?v=78Dr_Dz7GvI

Hope that fixes your problem.