I'm trying to focus stack in Photoshop using Auto-Align and Auto-Blend. However, the results are pretty poor. I don't understand why PS is interespersing segments of out-of-focus wire between segments of in-focus wire. If it just used the same layer/photo for those segments, it would be much sharper.
Are these results to be expected from Photoshop? Should I instead use other software to perform focus stacking?
Did you auto-align before you used auto-blend? Even if you shoot from a tripod, you must use auto align. The reason is that changing focus at macro distance also changes the subject size, so auto-align must correct this first.
To answer your second question: Photoshop only changes the layers if you select that option in the Auto Blend dialog. That is the 'Seamless colors' option (I'm typing this on my iPad, so I don't know the exact words).