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A little research on this issue turned up the following:
Possible bug on compare Autotrace results panel
The change to display even those statistics with zero values was intentional in order to avoid a bug in Autotrace comparisons.
As for the ordering of statistics, they are retrieved from the database in name order but then placed into an unordered HashMap, so the display order is unpredictable but usually acceptable in that large ranges of the statistic names tend to remain ordered.
I'll ping the developer so both of these issues can be taken under consideration.
Thanks for reporting them,
SQL Developer Team
Ah ha! OK, I don't know why I didn't see this before, yes I now see the sort order. I just missed the fact that there are upper case and lower case. Doh. Well at least now I can see how to find the stats I'm looking for. I look forward to seeing the new sort order thought so they sort in a more human natural way at least.