My best guess is that, by also forcing you to include your TV into the Activity, the Harmony software will create a mix of Commands from both the TV and the PS3, which will differ from a PS3-only Activity.

Please check that the Commands for at least the Left, Right, Up, Down, OK and Menu buttons in that Activity point to the PS3 Commands listed for these buttons in this table:

https://www.iospirit.com/support/faqs/remotebuddy/category/23/Hardware-Harmony-Smart-Control/entry/265/-/

Please also check that the Activity has been assigned to one of the Activity buttons (you may not be able to activate it via the remote otherwise):

https://support.myharmony.com/en/customizing-the-three-activity-button-keys#keyboard

Another thing that may be worth trying for troubleshooting is to use the PS3 device in "Device Only Mode" as suggested by Logitech here:

https://support.myharmony.com/en/using-harmony-in-device-only-mode#app

Hope that helps, 
Felix