Thanks Wolfgang. Clearly that fixes the problem. I also came up with another solution which avoids the need to define a MyChapterCommand, by first setting up the normal chapter as:

\setuphead
  [chapter]
  [header=empty,alternative=middle,style=bold,numbercommand=\groupedcommand{}{\blank[2cm]},after={\blank[3cm]}]

and then setting up a mychapter as:

\definehead[mychapter][chapter]

\setuphead[mychapter][header=empty,alternative=middle,style=bold,numbercommand=\groupedcommand{}{\blank[2cm]},after={\blank[.5cm]}]

That gives me the result I am after as well as maintaining the style of the standard chapter head.