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Recently upgraded remote buddy to 1.18, but not Lion. I have an unpatched version of Snow Leopard. Since that time I find sometimes the BD Remote is not responding. If I switch programs to RB itself, then I can usually start to open the menu again. Switching away and things work again. Otherwise I will restart RB program, and it may work.
The 3 behaviours I am using are 1 default behaviour (a custom), Spotify, and Mplayer OS X extended. I started using the Mplayer behaviour recently, about the same time as updating to 1.18. The first 2 behaviours I have been using for a long time before upgrading, and without any issue.
Its funny, because when it happens it seems just exactly like the batteries have died in the remote. So I switch to the RB program via the keyboard, CMD+ALT, I to get things working again.
At the moment, its a sporadic issue, with no explanation. I really can't be sure what is happening to trigger this problem. It has only happened about 4 times so far and without any kind of system sleep or reboot. This seems like a tricky problem. May just roll back to a previous version of Remote Buddy if its anything do with this new 1.18 release.