I have sucessfully run my scripts with no problems.
Here is what I have done.
I basically run my usrlogon.cmd file that maps out the main drives , the terminal server home drive and the users profile drive. I copy some files out to the users Terminal server home drive and then I call the kixstart script.
I have been using 3.43 for a wile and just basically have it in a Windows System directory.
All I do in the CMD file is a line like:
c:\windows\system\kix32.exe c:\scripts\logon.kix

I have yet to have a problem with it running