I have an application that when installed locally it runs in the systray. While running if you press alt+n the application pops up and you can use it.
When I ThinApp the application, the alt+n functionality does not work.
Would this be considered Windows Shell Integration that ThinApp does not support?
Did you put the package in startup folder?
The problem is not launching the ThinApp, but once the ThinApp is launched the user should be able to hit alt+n and the application should pop up.
For an application running in System tray there may be a 'Global Hook Dll'(hook.dll) or any other Dll file that is supporting the application using the Hotkey 'Alt+N' , in this case find which Dll is being used (this can be done using a tool-sysinternals proc-mon) register it through 'ExternalDlls' option in your package.ini the 'Alt+N' hot key functionality should work for thinapp'ed application as well.