Matrix displays the same category twice

I've come across the same problem today and managed to solve mine.  I know you never got a solution to yours, but my issue was the categories were ordered by different values.  So, if you've used "Sort by Column" for instance on your Question name, and you have different values for the ordering (on the same question), it will show the category multiple times for each order item.
Interestingly, when you make it a category you could drill down on, when you expand it, it will expand all categories of that name as if they were one.