OK I got it fixed, it was copying the games to the SD card and not running them.

i did this now. it updated from 4.4.38 to 4.4.45 (i think ;) )
but no effekt.

still got the up/down issue and when i change this in retroarch, I cant save this configuration.

shouldn't emulationstation automatically create a working config (RetroPad) for RetroArch, when I do the config in RetroPies Input dialog?

so there are 3 issues:

why was up/down wrong in RetroPie after the update? (ok, not that important since I could fix this easily ;) ) why can't I save a config in RetroArch? shouldn't ES create the right config for RetroArch without any further action?