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
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