Could it also have something to do with it not raining, no matter what time of year?
My thought is that when it rains heavy enough to be used, could that water be mixing with that bottom layer and making it less noticeably smelly.
Yes that could happen also. Rain water is colder than the pond in summer. As it goes in if enough volume because it is colder it will sink and effect the thermocline. Problem is that can lead to a turnover and fish kill.