If the script runs every time when launched manually after logon, then it can't be the script. Well, not quite, the is the issue of Wintendos and HKCU. See the FAQ section.
As for 'SetTime $Server3', in an AD environment, you must not intervene. AD does it's own timesync.
You also failed to post the logon.bat file you use to launch KiX, nor do you mention if KiX is run locally or from the \NetLogon share. It is also important to know if you have any other protcols and clients like NetWare.
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Give a man a fish and he will be back for more. Slap him with a fish and he will go away forever.
