My process is this:

Water stop bath;
Alkaline fixer (Formulary TF-4);
5 minute rinse;
Selenium toner;
15 minute wash.

From what I've read, one of the chief causes of selenium staining is residual acidity from acid fixers (i.e. most rapid fixers). Certainly, since I've begun using TF-4, I've not had a stain. Plus, it eliminates the need for hypo clear.