A couple of things could be happening here.
My.ini shows default engine = MyISAM. that's OK. So, if initialization of InnoDB engine fails, the server will still run, just InnoDB won't be available.
So, first up, take a look at what engines are running. Login with mysql commandline.
mysql>SHOW ENGINES;
Is InnoDB listed? Your my.ini file shows that it should be. If it's not there, take a look in the errorlog to find out why it's missing.
The error log will be in
C:\ProgramData\MySQL\MySQL Server 5.5\Data\<hostname>.err
C:\ProgramData is hidden by default. You'll need to unhide it if it's not visible.
The error log is plain text. Open it with Notepad (or some other text editor).
The last startup attempt is at the bottom of the file. What does it say about InnoDB, and ib_logfile(s)?
Good luck,
Barry.