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Hi Felix, 
I am having an issue where i can use my PS3 remote okay for the first time after initial start up, however once the remote disconnects it will not reconnect without first removing the batteries from the remote, then reinserting them. After this i can then press a button on the remote and it will reconnect, but again only once without repeating this each time it disconnects.
My preferences under Pref > Hardware are as follows: 
General 
Search for paired remotes on startup - Yes 
Display pairing instructions - Yes 
Display status messages - Yes 
Power Saving 
Automatically disconnect remote after inactivity of more than - 20 minutes 
Disconnect remotes when computer goes to sleep - No
I am running RemoteBuddy 1.22.1 under OSX 10.8.2 Mountain Lion.
I have followed the pairing advice under the PS3 remote FAQ and paired the remote successfully.
I am still under the initial trial of RemoteBuddy, but will purchase a licence if we can work this out - as when it works it's fantastic.
Thanks, 
James