This is an as-of-yet unknown issue and I can't reproduce it with Remote Buddy 1.16.6 running on OS X 10.6.6 on a Mac Pro.

The following information is absolutely essential to get an idea of what might be causing your issue - please provide it: 
1) Which version of Remote Buddy are you running? (please look it up under "About")

2) Which version of Mac OS X are you running? (please look it up under "About this Mac")

3) Which Mac are you using?

4) Please send a screenshot of 
a) Remote Buddy Preferences > Hardware > Bluetooth Receiver 
b) System Preferences > Bluetooth 
to info iospirit.com.

5) Which button (or button combination) do you press on your BD Remote to connect to your Mac? And for how long?

6) When did you buy the BD Remote you're having this issue with?

7) Since when did you use the BD Remote with Remote Buddy?

8) Since when did you start seeing the issue you describe?

9) Did you try with a completely fresh set of batteries? The BD Remote can behave very randomly when the batteries are low in power. Please keep in mind this is a Bluetooth remote and batteries can get empty *a lot* faster than is the case with infrared remotes. So even if you replaced the batteries two days ago, you really should try with a set of new batteries today - to simply eliminate this as a variable.

Best regards, 
Felix Schwarz