Maybe the environment is losing the handle to the file.

Just for trial, try keeping a copy of all the files on the LOGON share and calling all of them from the Logon share and see if Windows 9x still has a problem finding them.

Do they work if run from a command prompt on Win9x instead of the logon script?

You could also try KIX32.EXE /D yourscript.kix

Then see if anything more specific comes up in the code. Maybe a run or shell statement that Windows NT/2000 is okay with that Win9x is not.