USRLOGON.CMD not running on 64 bit CPS4
Filemon showed that its not running from %windir%\system32 but is being looked for in other directories.
The CTXHIDE.EXE in 64 bit citrix does not use the normal c:\windows\system32 location, this is possibly because its running in wow64 as the component is likely still 32 bit.
32 bit apps that make calls for files are redirected to C:\windows\syswow64 for their files
To resolve the issue i placed my custom copy of USRLOGON.CMD file in either c:\windows\syswow64 or c:\windows
There is a Citrix article on this issue.
http://support.citrix.com/article/CTX108901