also setting "-d session.auto_start=0" in the binary command line in the first line of the script doesn't solve the problem, yet doing so when calling the script in the "php [script name]" form from the shell does. in both cases setting the entry in the ini file solves the problem completely.

Please try using this CVS snapshot:

  http://snaps.php.net/php4-latest.tar.gz
 
For Windows:
 
  http://snaps.php.net/win32/php4-win32-latest.zip

Attempt that enables output buffers flushing is rejected, so it won't fix.

So this is indeed a bug ? Great.

In the meanwhile, for anyone else who is expiriencing the same problem I recommand the solution I found for myself, until more light is shed on this issue. When you configure before the compilation, use the --with-config-file-path=[path] switch, and compile the apache module with let's say /etc/php/apxs/ and the cli binary with /etc/php/cli/.
That way you can tweak the configuration independently for each build, and disable things for the cli without interfering with the web server's work.

Your output is buffered since there is "trans sid" buffer due to sessoin_auto_start=1. It prevents output buffer flushing.

BTW, there is flush function called ob_flush(). It differs from flush(). However, ob_flush() is also broken from the beginning and it will _not_ be fixed. So don't use it.

Don't try to use ob_implicit_flush() to flush output buffer, it does not flush output buffer, but SAPI buffer. It will _not_ help to output buffer flushing at all.

flush() try to flush web server buffer and it does not help flushing output buffer contents at all.

If need to direct output, don't use buffers. i.e. don't use trans sid, char encoding tranlation, zlib output compression, ob_gzhandler compression, etc, etc.