Please note that Remote Buddy only forwards the IR signals to the Apple IR subsystem when using the Virtual Remote.

Which action is actually triggered by these events is still decided in the application that receives them (here: Plex). Please download the HID Remote SDK here:

http://www.iospirit.com/developers/hidremote/

It also contains a test application that shows a log of the events received through the Apple IR subsystem. Please check whether long presses get logged as long presses, there.

That said, some Harmony remotes - for whatever reason - don't support long presses for particular buttons (I noticed this with the red/green/blue/yellow buttons pretty often). If you assign the same "action" to, say, the Harmony's play button and the red button inside Harmony's configuration software, these models will only correctly send what's needed to create a long press button event for the play button, and not be able to do the same for the red button.

Depending on how you set up your Harmony, this might also be something to consider.

Best regards, 
Felix Schwarz