Sometimes I have to create a published application that just starts Windows explorer.exe.
As explained here this does not work as expected: http://support.citrix.com/article/CTX128009
I have had no luck with Method 1 (ApplicationLaunchWaitTimeoutMS) even though the described hotfix should be part of rollup 1.
But method 2 works for me (LogoffCheckerStartupDelayInSeconds):
You can set this during deployment in you MDT or SCCM task sequence:
reg.exe ADD HKLMSystemCurrentControlSetControlCitrixwfshellTWI /v LogoffCheckerStartupDelayInSeconds /t REG_DWORD /d 16 /f