On Windows the Windchill shell environment must be recreated by your batch file. You can't use "Windchill Shell" because it breaks the 'link' to your batch file and won't let you run any subsequent commands. Iposted a solution to this last spring: http://portal.ptcuser.org/p/fo/st/topic=16&post=106961#p106961
Using this technique you can batch script Windchill commands and call your batch file via psexec.
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Really glad I found this thread and Matt's solution. Currently having some Windchill issues, as a temporary work around need to use a windchill shell in a batch file, couldn't figure out how to do this until I came across this post. Very disappointing in when I asked PTC tech support they would not offer any assistance, especially when it was related to an open case.
Note that in addition to 'windchill.exe' 10.2 (at least M030, I forget about older MORs) and higher, contain a 'windchill2.bat' script that's purely a Windows batch script. I believe it contains additional options that just might be helpful here.
On Windows, the Perl-based windchill.exe still remains "the" windchill command for various reasons backwards compatibility reasons, but "windchill2.bat" is available -- except in InService where windchill.exe has been replaced by windchill.bat, which is just a copy of windchill2.bat.
On UNIX, the windchill command's implementation was switched from Perl to Bourne shell.