@gidgreen When Q2A is set to use hyphenated tages, these are stored in the words table in their hyphenated form. When Q2A is then changed to use comma separated tags, the hyphenated versions of these tags are already in the words table.
In other words, using Q2A default setup, enter a tag "foo-bar". Then change Q2A use use comma separated tags and enter a tag "foo bar". The words table will contain "foo-bar" which will not match "foo bar". Also, when typing "foo" into the tags field, tag matching will not suggest "foo-bar".
I hope this explanation makes sense. :)