Definately there's a head cat situation. In my house, its Allen, followed by Harry (who is starting to work up the nerve to fight Allen for top cat position). Sounds like some territorial issues have arisen over the litterbox.

Rule of thumb with litterboxes: one box for every cat plus one. So two cats should ideally have 3 boxes. I have 6 cats, and 7 boxes. I say ideally because it isn't always something we can do, but its what would be best. One box for two cats is really just too few - and you're finding out the outcome as to why. For the longest time I resisted the rule of thumb thinking that if two of my boxes were larger and I scooped 3 times a day it wouldn't matter.... it does. My life has gotten sooo much easier with the additional boxes. Feline relationships got better.. Who knew!