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Thanks for asking.
Pairing an Apple Remote is very different from f.ex. pairing a Bluetooth remote: the Apple Remote will work with Remote Buddy out of the box - and pairing really just enables a filter so that henceforth only IR commands with the ID (0-255) of the Apple Remote used for pairing will be accepted.
You can view the pairing status at Remote Buddy Prefs > Hardware > [Keyspan IR Receiver].
If the Apple Remote doesn't seem to work:
1) try unpairing the remote in the aforementioned prefs (if paired, this option will be presented to you there)
2) consider replacing the battery. Unlike its plastic predecessor the aluminum Apple Remote does not send a low battery warning code and sometimes sends incomplete or crippled IR codes when power is low.
3) be sure to try pressing the Menu button, which in most situations should enter Remote Buddy's menu.
- Felix