I don't know the background of your Jack or how old he is, but our kitties were feral rescues, and they liked to sleep in the box sometimes. They used to sleep on dirt, so maybe it had something to do with that? They also liked to play in it (thank God they grew out of that one!)
I don't think Jack's such a weirdo - I think all cats are just crazy!
Have you had him for long? Sal used to hide in his box every so often. He seemed to find it reassuring. I actually picked him at the breeder because he was chasing around a female half his size to play and when she turned around and hissed at him, he ran and jumped in the box. He seemed to have grown out of his Freud phase. He has long hair so I was always a bit yucked when he laid in there!!!!
I've had him for 7 years and he's about 9 years old. There is nothing skittish about Jack. He is bold yet loving towards every person he meets. I get jealous because I truly think that I could disappear tomorrow and he'd just latch on to whichever person was most convenient. Butthead.
I don't really know his background. We got him from a rescue and he was classified as "semi-feral." There is nothing feral about this cat at all.
I get yucked out too, because he'll snooze in the catbox and then jump up all over me. Pass the Purell!!!
We used to have a lot of kitties do this in the kennels where I work.. We've gotten them to mostly stop laying in the litter-filled boxes by either putting in the cat 'cubes' they can hide in, or putting in a second box with a blanket in it.