A more explicit minimal example of the problem:


\setupheadertexts[section]
\setuphead[section][%
    placehead=empty,
    before=,
    after=]
\setuphead[subsection][%
    placehead=yes,
    before={\blank[line]},
    after={\blank[line]}]

\starttext
\showframe
\section{My section}
\subsection{My subsection (whitespace before: problem)}
\input knuth
\subsection{My subsection (whitespace before: fine)}
\input knuth
\page
\subsection{My subsection (NO whitespace before: fine)}
\input knuth
\subsection{My subsection (whitespace before: fine)}
\input knuth
\stoptext