Check your signal readins for the 99(c) and 103(c) satellites, which is where most of the HD is located at. You should have readings in the upper 80's to lower 90's on a clear day, if not the dish might need a slight realignment.
Also, the Ka band that's used for the 99 and 103 satellites is more sensitive to rain fade, which is why having the dish properly aligned is more important then for the old SD channels.