My understanding is this:
1. Satellite has problems with thick clouds. Your typical thunderstorm contains 500,000,000 Kg of water vapor, so it's no surprise that dense clouds will screw with some wavelengths of radio waves. Take a look at the weather radar when you lose reception and see if you see anything to your south that could be in the way.
2. I'm betting the reason some channels are fine and others are not is that you have a system like my family's that uses multiple satellites to give you all of your channels. My guess is that you'll get spots in a cloud formation that are dense enough to degrade the signal lower than the error correction can deal with. At that point, you lose the signal. However, the different satellites are several degrees apart in the sky, so a spot could be in front of one satellite and not the other and you only lose the channels from one satellite. I think the way that Direct TV works is that the local channels, foreign language channels, and HD channels are on one satellite and everything else is on another.