I was trying to modify Krita shortcuts in order to make them work as I'm used to. The Configuration Widow pops up, everything is fine... Also I'm able to introduce the new shortcuts without a problem. However, as soon as I hit the OK button and the widow closes, Krita does not apply those changes. What is more, when I open the configuration window again, the shortcuts remain as default.
Sorry, I found someone else had reported this bug alredy... Mea culpa
This got fixed in master, so it should be fixed in the next release build! If not, don't hesitate to reopen :)