When starting scripts for seamless apps from USRLOGON.CMD/USRLOGN1.CMD the script fails to run.

This is due to the CtxHide.exe process causing issues.

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon]
"AppSetup"="CtxHide.exe UsrLogon.Cmd,cmstart.exe"

Remove CtxHide.exe from the AppSetup value:

REG ADD "HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon" /V AppSetup /D "UsrLogon.Cmd,cmstart.exe" /F

Usrlogon.cmd Does Not Execute on Presentation Server for Windows x64
http://support.citrix.com/article/CTX108901

http://forums.citrix.com/thread.jspa?threadID=272268