Strange problem! The first thing that comes to mind is they may not be mixed thoroughly. Are you stirring them enough? I'm sure you are, but you never know! Are they old bottles, and perhaps the paint has separated from the medium or some other strange transformation has taken place in the molecular structure of the paint? Left in the sun, too hot, too cold, that kind of thing? I've never experienced such a problem, so I can't give you any first-hand advice.
Anyone else with any ideas?