I'm also having this issue (MacMini: Mac OS 10.5.8, Remote Buddy: 1.16.5, Plex: 0.8.5, white Apple remote)

I have Remote Buddy set to run a script that launches the switch inputs on my receiver and then start Plex when the menu button is held (which works). I also have scripts to change the volume on my receiver when the +- buttons are held (which also works). The problem is that as soon as I assign a script to either Up (hold) or Down (hold) navigation stops work (it works occasionally but for all intents and purposes is broken)

I'm still on the 30 day trial, I *really* want to buy this program but I really need to be able to change the volume on my receiver too.

thanks 
bryan