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Please note that Remote Buddy only supports devices listed on the Hardware page. Devices emulating these devices may - or may not - work, depending on how close they are to the original. Officially, these are not supported.
For Bluetooth remotes, Remote Buddy uses several clues to search for and identify devices you want to add. One of the primary clues is the name the device advertises as. This name, once retrieved, is cached by OS X - and there’s usually no need to query the device for its name again, if it has already been retrieved, since - for the devices supported by Remote Buddy - it never changes.
If you are switching between PS3 BD Remote and Wii Remote emulation on your Harmony, it’s bound to advertise with different names. Problem here: OS X may still report the respectively other device’s name from the cache (f.ex. the Wii Remote’s name), while the hardware is now emulating a different device (f.ex. a PS3 BD Remote). If this happens, the device will behave differently than what it was recognized as - and pairing and/or usage is bound to fail.
Best regards,
Felix Schwarz