Haven't seen this problem yet.Note that the consoleless version isn't very useful on Windows 9x unless you use LMSCRIPT emulation, because otherwise you will always have a console anyway. This is caused by the way logonscripts are handled on Windows 9x.
Also note that you may need to launch the batch/executable using START /w, otherwise the calling batch may terminate prematurely, and the connection to the NETLOGON drive may be lost before the script completes.
Kind regards,
Ruud