My controllers are working now, but has nothing to do with the RC3. I found out the following by trying it out. It was just a setting that you can't change in Amiberry's GUI. Here's what I've done now:
In the folder /recalbox/share/roms/amiga1200 I created a file named .uaeconfig.uae
IMPORTANT is the POINT in front of it, otherwise the file will not be loaded!!!
In this file I have only two lines in it, which will be overwritten by the default configuration:
show_leds=false
amiberry.use_analogue_remap=false
The use_analogue_remap is normally set to true and therefore my PS2 controller or CompetitionPRO didn't work.
Maybe this will help others too!