You ask good questions. To which I don't really have answers. We've never dealt with using ANATicor on people with WM atrophy. In such a case, I would definitely not rely on the built-in AFNI 3dSeg program for finding the WM -- at least without some looking at its results to make sure they are "reasonable" -- and how one defines "reasonable" in this context I don't know.

I can't say we've seen the creation of WM blobs by ANATicor. If this is common, but only in people with WM atrophy, then that is also an interesting effect. Does it also occur if you use the COMPcor-like analysis method available in afni_proc.py instead of ANATicor? (That is the "-regress_ROI_PC" option -- I've never used this option myself, so if you want to try it, you'll have to pester Rick Reynolds.)