I have tried rebooting roughly 5-6 times now and every time I connect the DS3 it has the key map of controller 2. However as I see it this is not a big issue. I can easily remap the keys in DrNokSnes.

What's troubling me is the strange behavior of the N900's user interface when connected. It's almost impossible for me to select options in scroll-down lists (i.e. when doing the key mapping in DrNokSnes). When I try to select such an option/button it scrolls away. Also when scrolling down a list it's like the scroll function live it's own life. Actually it seems like all GUI components w/o scroll-function is working ok.