Setup: Windows 2003 R2 SP2, XenApp 5.0, Seamless Applications
Problem: A seamless session would launch for the program, then instantly quit again with WFShell stuck on ‘end process’ – the application would work once after reboot (intermittantly)
The seamless window would just disappear with little in the way of errors logged locally.

Resolution:
Turned out to be one of the dll files being launched by the APPInit_DLL registry entry was crashing the Session

[HKEY_LOCAL_MACHINESOFTWAREMicrosoftWindows NTCurrentVersionWindows]
“AppInit_DLLs”

Remove the troublesome DLL/s from here one by one until the session stopped crashing
(in our instance I removed all dll’s)