Lately we saw many complains of how MySQL Config Wizard works.
Most of them are just special case of bug #42820 verified some time ago. I though it has trivial workaround, but one of users complained he read a lot of articles related to this bug, but nobody pointed the workaround.
So here you are: if your my.ini is broken after update, copy old saved configuration file (it should be file named my.ini.bak or similar in the installation directory) or fix new one manually, then don't run Config Wizard again, just manually start the service.