What Are These Spots ?

These images were made with my K-30. I found a black spot on one of my images of a cloud when enlarged. Thought I would check for bad pixels. The images below are not the one where I found the black spot, but these are new test images. Will describe each as a caption. Thanks for all help

Shot #1 of a cloud modified with Levels & sharpened to enhance irregularities

Flash shot #1 of a white card enhanced with levels & sharpening

Flash shot #2 of a white card enhanced with levels & sharpening. Seems the two card shots reveal the same pattern.

Shot of clouds #2 showing no irregularities other than a far away bird

I don't understand this, no irregularities as other shots I looked at had dark spots, but not always in the same places. I believe the spots appeared the same in two shots, but not all. The white card shots are crops. All help will be appreciated.....Dan

PS.....In the mean time, a dust speck appeared on my focus screen. Tried brushing it off and the problem got worse. Depressing.