I've been searching for the last couple of days and can't seem to find a solution to my problem. Here is my setup:

Late 2012 iMac (no built in IR) 
Twisted Melon Manta receiver 
Plex Home Theater 
Harmony 650 remote - "Apple TV" setup as the device in this scenario 
Aluminum Apple Remote

Essentially what I want to accomplish is to regain control of Plex exclusively with the Harmony Remote now that my new iMac doesn't have a built in IR receiver.

I'm currently on the trial version of Remote Buddy to see if it will accomplish what I want. I have been able to get everything working almost perfectly by setting the global mapping to the Virtual Remote button presses of the Aluminum Apple Remote. My settings mirror what you've described here:

http://www.iospirit.com/blog/article/131/

I have created a custom keymap.xml file in Plex so that these virtual button presses are translated into my desired actions in Plex HT. I have Plex configured to use the standard Apple remote profile and to allow launching of Plex with the Remote.

Using my Aluminum Apple Remote, I works flawlessly. All short and long button presses are translated properly.

When trying to use my Harmony remote, the long button presses are sent as short presses. For example, when playing a Full Screen Video, long press menu should send Stop, instead it sends OSD (which is configured for short press menu).

It seems that the problem can be traced to how Remote Buddy is interpreting the long presses from the Harmony as this same Harmony device profile will control my Apple TV without error (including short and long presses), and that my Aluminum Apple Remote works in this setup perfectly.

Any help you can provide will be very much appreciated! Thanks 

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 

Conversely, the Aluminum Apple Remote recorded all button presses (short and long) correctly every time. In addition, the Harmony as tested will control my ATV 3 without error in both short and long press commands.

I tried re-mapping the Menu button to various other buttons on the harmony but none were able to send the hold press command correctly. I've tried mapping it to Menu, Prev, Volume Up, Stop.

I also tried altering the inter-key delay (from 0 to 1000) and repeats (from 0 to 5) in the Harmony software but none of that seemed to impact my results.

Any other ideas?