Hi,
it seems to me the mysqld binary, compiled from sources, is placed in
libexec/ directory, but you binary distributions contain it in bin/
directory. I know that at least once with 4.0.9 linux binary dist I've hit
a case, when mysqld was expected in libexec but wasn't (I mean the rc
script supplied with distribution expected the binary in libexec, or it
got compiled into the binaries as default value ... I guess).
How-To-Repeat:
I don't have time right now to reproduce this, I think pointing this out
should be enough to get rid of libexec directory at least.