For the record, these are not my macros.  Aren't they yours?  Anyway, the only thing I changed from what's on

http://wiki.contextgarden.net/SlideWithSteps

is I changed \eject to \page[yes] and I changed \phantom{ ... } to \setlayer[StepsHiddenLayer]{ ... } where StepsHiddenLayer is a "hidden" layer.  Like you said, the problem seems to be that I cannot do

\setlayer[StepsHiddenLayer]{ ... }

on a "row" of an align.  Surely there is a solution to this.  I will post it now to a separate post.

Troy