Well i'm dumb. Had the controller on directinput instead of xinput. Update had nothing to do with anything. Sorry about that.

My advice is to not use 'Save on Exit' and use Core/Game overrides for changes you want to add to the controls. If you want to have a global configuration setting applied to all Libretro cores, open RetroArch from the RetroPie system in Emulationstation, make your changes there (it will modify the global RetroArch config file) and use Save Configuration to save those changes. More details about the configuration structure used by RetroArch in RetroPie can be found here.

Just tried a few with the (re-)modified configs/all/retroarch.cfg : Atari 800 now uses the analog stick only - with whatever assignment (digital or analog) N64 seems to do the right thing now: only the analog sticks work In PSX only the dpad works So all in all, quite a weird combination which doesn't seem to make too much sense. @mitu said in (PS3) Controller configurations across different emulators: Actually, not all is lost (well, not so dramatically). While it may not be an option for the emulator, you can trick it by re-modelling your controller - Xboxdrv. It does require more setup work though. Will see. For now I guess I will stay with the analog stick working as dpad option. Either way, only one emulator does it wrong then (N64) besides PSX which seems to do it wrong all the time, while then at least I have the choice of using one or the other control with all remaining emulators. By the way, after switching off this analog=dpad mapping, In Vice still both controls worked, which makes full sense because in Vice's configuration screen you can define the dpad and analog controls separately - in a working manner ;-) EDIT: The challenge for the PSX emulations is probably the fact that the analog version of the PS controller was released "belated" in 1997, a long while after the PSX was released (by that time only with a digital controller). There weren't too many game titles also which actually supported the analog controller feature, and those who did obviously did that with regional limitations: https://en.wikipedia.org/wiki/Dual_Analog_Controller All in all a relatively complicated topic, which might explain in a way why analog support works quite well in the N64 emulations (where an analog controller was provided natively) and not so well in the PSX ones. There for the most part, it seems to depend on the game itself and even its country code, if Dual Analog Controller or even Dual Shock Controller support actually works. The latter one does for me in a few games, e.g. Driver II, but then again the real analog stick support I couldn't get to work, neither for this nor any other PSX game.

OK, so reflashing the install seems to have worked. I'm not sure if the original 64gb microsd was too large, or if something else I did messed things up, but this time around I wasn't asked a second time to initialize my controller settings, and I was able to get a few minutes of Super Mario World running with the controller functioning properly. But, thanks for the help, no wonder nobody else was having these problems.