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Hi Felix,
I am having this exact same issue. Rather than opening another thread i though it would reply to this one. 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
My remote disconnects and then will not reconnect without removing the batteries.
Thanks for your help.