More info here (tx MG)
http://notes.sagredo.eu/en/qmail-notes-185/installing-dovecot-and-sieve-on-a-vpopmail-qmail-server-28.html#comment995

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The qmail-maildir++ patch, which is fetched and enabled in case the
MAILDIRQUOTA option has been enabled miscalculates the file size in
qmail-local.c because the first two lines of the mail file (Return-Path and
Delivered-To) are not taken into account. As a result, the filesize
part of the S=<filesize> component of the Maildir++ compatible filename
is always too low. This hasn't been noticed for many years, since the
impact on quota calculation was negligible (typically less than 100
bytes per e-mail). I stumbled over this, because mail/dovecot2 2.1.7 is
actually comparing the value of S= with the result of stat and ends the
connection to correct the problem. This is also affecting any other
program using Maildir++, so this definitely needs to be fixed. The
specification of the Maildir++ format clearly states that the S=xxx
should match the size of the file (see also
http://www.inter7.com/courierimap/README.maildirquota.html).

The following line in the patch is the root of the problem:

s += fmt_ulong(s,st.st_size); *s++ = 0;

which should be:

s += fmt_ulong(s,st.st_size+rpline.len+dtline.len); *s++ = 0;