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I'm sorry, but I'm having problems understanding the question.
If I understand you correctly, you've set up BetterTouchTool to perform actions when you press a button on your Apple Remote. In this context it's important to note that input from the Apple Remote on OS X can only be received by one third-party application at a time. If you have installed Candelair, Remote Buddy will receive all Apple Remote button press events - and can forward them to other applications via its built-in Virtual Remote. If you don't have Candelair installed, Apple Remote button press events will go to whichever third-party application asks OS X for it, first. If that's not Remote Buddy, it'll inform you about which third-party application receives all Apple Remote button presses instead.
I'm not sure about the part of your question mentioning keyboard and mouse problems. Fact is, however, that Remote Buddy only uses public APIs as documented by Apple. It can't have any effects on your ability to use your mouse or keyboard to control your applications, because it doesn't use any APIs whose use could have such an effect. I also have never received any reports about such issues.
BetterTouchTool, on the other hand, probably makes use of the CGEvent(Taps) API to allow you to re-route or discard input coming from your mouse and keyboard. So if you suffer from issues with mouse and keyboard input, maybe that's the result of just how you configured BetterTouchTool.
Best regards,
Felix Schwarz