It looks like $SubOption is being treated as a Hash reference.

No, but $Config{$Item} is. You're printing the values of the %Config hash, which are either hashrefs (in the case of sections with foo=bar lines) or scalars (in other cases). Nothing to be surprised at.

BTW, you'll be running into trouble when you have stanzas in your ini file which contain multiple lines without = in them (e.g. multiple email addresses in [Notify]). You might want to consider changing your data structure.