Looks like early blight. Remove and discard in the garbage.

Two week later and new growth on the plants look fine. Removed affected leaves and the plants no longer look sickly. They are growing quite quickly and thickening up well.
When it rained again, some of the lower leaves turned colors and again looked odd. This seems to happen after it rains for awhile with no sun.

Still believe its early blight?

Can we diagnose your spots? SURE!!!

Let's see. You're either a leopard, a jaguar, a young deer, or we all have eye problems. :>)

I think you've got it right. Weather related. Intensity of the green color will vary somewhat with the amount of direct sunlight the plants receive. Plants will tend to want to shut down some areas if the flow of nutrients and energy are not adequate. A foliar feed can sometimes offset this.

Ted