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I worked at an animal shelter over the summer, and finding cats sitting in or sleeping in their little boxes was actually quite common, believe it or not. Cats sometimes see their litter box as a "safe spot", which is why most of the cats in the shelter did it (at least, that's what the vet tech told me when I asked her about it). Maybe something stressed your kitty out? It can also mean they just aren't feeling well, which would make sense with the IBD. If he's eating, drinking, pooping, and peeing normally, things are probably okay. If not, time for a checkup with the vet! Sometimes males spend extra time in the box if they have a blockage in the urinary tract, but you'll usually see them squatting, straining, or scratching around if that's the case.
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