Hi Hubert, thanks for posting in our forums.
If you do not have any important information you want to save at your 5.0 folder, you can delete it safely after restarting Windows. If that does not suffice, try to do it in safe mode as you said.
For the problem with Notifier, I'm quite sure it is not an issue related to the my.ini file (thats is a server file only.) but rather a problem with the settings.config file which may be corrupted. It present in the %Appdata% folder (which depending on your OS version could be: for Windows Vista thru 8.1 and C:\Documents And Settings\<YourUser>\Application Data\Oracle\MySQL Notifier\ for Windows XP; older versions are not supported.) If the file is corrupted the easiest solution is to delete it (quit/exit Notifier first to avoid locking the file). If you're running the latest version of MySQL Notifier available, the file will be recreated automatically when you run Notifier again.
Normally, if you:
1. Open a Run command and type the following: %AppData%\Roaming\Oracle\MySQL Notifier\
2. Delete the settings.config at the mentioned location.
That should be enough to get you thru the Notifier startup problem, follow the extended instructions from the link in below if that did not suffice.
(here it also explains how to delete ghost services, if any):
http://forums.mysql.com/read.php?173,596813,600694#msg-600694
I appreciate your concern on repeated topics and sanity of questions inside the forum. We're somewhat limited by the current forum's system since posts older than 90 days are closed automatically without any room for further discussion after that point, we appreciate your understanding, patience, and support. Thanks!