If you setup a roku device on your harmony, or any other device on your harmony that exhibits this behavior, this guide will help you solve this issue.
In certain settings, a device might interpret one remote control press, as two presses. This is because the harmony remote control has many advanced settings, and on the roku devices and similar profiles, the harmony is set to send multiple keys per individual press. This is likely due to the fact that the roku device wants to be sure it's receiving a signal, so it waits for many to arrive.
However, flirc and the connected machine might interpret this as multiple independent clicks. (it actually thinks your holding the remote control button down long enough to start repeating on the host operating system).
Let's solve this by going into the harmony settings.
Select the remote control in the devices tab, and click settings.
Then click 'Troubleshoot' on the next menu and hit next
Then click 'Media Center PC responds to some commands either too many times or only occasionally"
Hit Next and Select '0' on the following screen
That's it! Now update your remote control and wait 10 minutes for harmony to get this one number updated (sigh).