correct me if i were wrong. supposedly, the cpl will only allow lights of certain polarity to go through, while normal sunlights contain lights of all kinds of polarity. your cpl will work the best when the lens points to sky that is 90 degree (perpendicular) from the sun (perpendicular), and filters lights less when you point it more to the sun. theoretically, you always get less or equal amount of lights depending on the angle, doesn't matter what objects that is reflecting the lights.
here may be the problem, if you are using a cpl and you are using the sky as a reference for your middle gray (object to set for middle gray exposure), you MAY overexpose the cloud because lights reflected from the cloud may not get filtered as much as the blue sky. to compensate the darkened blue sky, the camera will ask for more exposure, while the lights reflected from the cloud do not get filtered as much as the blue sky, the cloud will become overexposed when you set the sky to middle gray under the cpl.