Sorry my glass sphere is off for maintenance so I can only guess what's wrong. Delete the es_systems.cfg located in Configfiles/Emulationstation and apply the update again. Then at least PPSSPP should work again because the recent version won't work in KMS mode.
About "WII" I guess you mean Dolphin does not start. Well without logs I have no clue what's wrong.Last but not least ALT+ESC closes Fluxbox windows so yeah it works. At least for me. And others. So what is still running after you hit ALT+ESC?
I tried to delete the es_systems but no luck!
could you advise which Log i should upload to get a better idea about the issue?