Nice another IT-guy who didn’t get it sorted out the first time… ;-)

But this one has finally success… I’ve no idea if it makes any sense what I did but my goal was to wake and sleep the MacMini and control Plex and its features… Finally it’s all working now! Hurray!!!

This is what I did to get the Harmony control the MacMini with Plex installed via Remote Buddy (BTW I installed Remote Buddy because of the sleep issues since OSX Lion) maybe some steps are not needed but I give you all I did:

1. Set Plex Preferences to use Universal Remote and quit Plex. 
2. Pair the 10 Harmony “virtual” remotes (150-160 except 156) via the Hardware option. 
3. Add 10 logical remotes for the just paired ones and map them to the ID’s of virtuals. 
4. Set the 10 logical remotes to the aluminum ones by clicking the name and select your remote 
5. In global mapping (I don’t need Remote Buddy for any other applications) set all the remotes to use the Virtual Remote buttons, for example Up => Virtual button press: Up and so on for all the remotes, this will take some minutes ;-) 
6. Set Plex Preferences to use Harmony Remote 
7. In the Logitech software adjust the power options for the Device Plex; I want to turn off this device when it’s not in use; A button on the remote for On, and a different button for Off; On – I don’t have the original remote, but I know the command that is used => Play; Off – I don’t have the original remote, but I know the command that is used => Sleep 
8. I also adjusted the delay settings, to Power-On delay 1500ms; Inter-key delay 100ms; Inter-device delay 500ms 
9. Update the harmony and try again, I my case with this settings it works like a charm.

I hope that this steps also can help you and others who are struggling with this issue.

Best regards, 
Melvin