Focus stacking less than perfect results - blurry splotches

Hey guys - doing focus stacks for some product photos and I usually get good results. I use a Canon 5DII w/ 100 2.8L Macro for nearly ALL of my product photos as I find it gives a true or more accurate representation of angles and lets me work in almost any sized room, generally.

If I have a unit that is about 6" deep or so I will stack maybe 5 - 6 photos from about a 3 - 4' focal length (I try and put the subject in center of the frame with about 10 - 20% of the view finder of space on top and bottom, if that makes sense). If I have a unit that is much larger, like 20 - 24" deep, I'll shoot maybe 15 - 18 stacked shots but am usually further back, so DOF is a little better. I always shoot f/8.

Every now and then, though, I get lousy results. Most of the time I get great results. I find when a subject has a large surface with little variation is when I have issues. For instance, see the images below -

Here is a good one:

IMAGE LINK: http://www.flickr.com …67031861@N08/10​068293793/

IMAGE LINK: http://www.flickr.com …67031861@N08/10​068159494/

IMAGE LINK: http://www.flickr.com …67031861@N08/10​068246756/

Well I can see how it would be hard for software to decide, for smooth surfaces with no edges or contrast, whether a given point is in focus or not. I don't have a solution for your problem; I would suggest doing it manually. CS6 allow you to load multiple images and automatically align them, which would probably help you quite a bit (you can either go to file > script > load as stack, or manually load the images in layers then select them all and go to Layers > Auto-align).