View Table grouping on Taxonomy terms
I've had this problem before too!  Very annoying.  ;-)  The reason that happens is that, by default, the list of tags are displayed as a comma-separated list when the node is tagged with more than one term.  The way you can change that settings in your view is to click on the field that is your term in the Fields section of the view and expand the 'Multiple field settings' which should exist for this field (since it's an input field that accepts multiple values.  

In your case, it would be best to select that only the first value is displayed like so:



That should work for you.  You'll see that the content type will still appear under all of its categories if it is tagged with multiple tags, but they won't be grouped in long lists with commas.  :-)

Let us know if this works!