Well that may be because of the cold.You know when its about to rain,it gets a bit of cold(Generally).So could be because of the cold that your knees start to ache.May be!

I have to second Tally here. If you have sensitive joints, you may be able to feel changes in barometric pressure.

Another barometric pressure-related cause of joint pain is “the bends”, a condition which affects divers who absorb nitrogen into their blood while diving and experience pain when they surface too quickly, as the bubbles of nitrogen expand in their blood stream. Cases of the bends have been recorded among construction workers digging deep holes and miners in deep excavations as well as among divers.

You’re not crazy. For me I can predict the rain in two ways. The first is in my knee. I had surgery a little over a year ago and have a pin in my knee. I don’t know why but it twitches and seems to do it before it rains. The second is that my lower back begins to ache. I don’t know what it is about the rain, but both also do it when the temperature drops and is cold. I’ve never paid attention to the actual degree of when my back or knee will twitch. I live in Michigan, so during the winter my knee will twitch if I am outside for more than a few minutes and back my starts to hurt.