Hey, i was having a similar issue after updating my binaries yesterday. It seems the default emulator for mame4all changed from lr-mameforall to “mame4all”. I presume the libretto version has the patches to make the ps3 controller visible..
Either way, the fix for me was to launch a game from emulationstation.. hit a key on the keyboard whilst it is loading (when prompted) and you should get the blue configuration screen pop-up.
Choose “1 Select default emulator for mame-mame4all”
then ensure “1 lr-imame4all” is selected.
This now works with my ps3 controller.. Though the downside is that this version has the nags and info screens enabled.
Hope this helps!