I finally could solve the "double trigger issue" regarding my Apple Aluminium Remote.
Like I initially suspected, the individual triggers were configured twice for the device Apple Remote, maybe because of a sync issue. Removing the duplicate trigger entries, solved the issue for me completely. The configured Apple Remote triggers are working again just fine.
I'm not exactly sure why, but for some reason I could not find the right menu for that configuration. I guess, I was not aware, that the old UI is still available or maybe the Apple Remote (legacy support) device was not available in earlier versions.
I'm quite happy, that I finally could solve the issue.
Thanks for your great work. I really can't imagine working on any of my Macs without BetterTouchTool.