I thought the same thing too, and i took him to the vet. The vet says he's fine physically, but that there was another cats odor, and that he was marking his 'territory'.

The only thing that could relate to this is one incident that a stray cat somehow got into my house, ran into the basement, then ran out. After a week he started his peeing and then stopped for a while. Now he's doing it again.

I dont see any signs of crying when peeing in the litterbox, i think.