photoshop - Why does my focus stack result in a blotchy background?

I've recently taken up photography with using a Canon 50D and thought I'd try some macro photography of flowers. Having researched the subject and read about focus stacking to increase the depth of view I've just taken a few sets of images and performed focus stacking in Photoshop CS5. The flowers have generally come out nice and sharp, however the backgrounds are all blotchy with different parts of the background being taken from different images. In all the tutorials I've seen for focus stacking none have had this problem. I know the linear changes towards the edges are due the the alignment process and will be croped

What am I doing wrong? Is there anything that can be done in Photoshop to correct the problem?