I just uploaded a build 9.23.42 with some new features and two small fixes and among the new features I included two queries getting high fragmentation info for DTA and MSGBOX dbs. Behind this query is a SQL script which is available only for 2K5 SQL Servers which get list of indexes where fragmentation percentage > 30, so these two queries won't execute on a BizTalk 2K4 Group for example.The tool however keep the old Detailed Fragmentation queries.
You have to keep in mind that the SQL query getting this Index fragmentation info can be long to execute so it is possible that the query will timeout after the default Query Timeout of the tool which is 30 secs. If output of these two queries is important for you, then you just have to increase the Query Timeout in the tool (avail in the Console version also); as the opposite, If you can avoid the result of this query, well..just unselect them in the list of GUI tool as they are both optional !
Note that when you increase the Query Timeout, it will impact so all other quereies as all the queries use the same global Query Timeout. Indeed, I did not implement Query timeout per query (maybe in a next version if there is really a need)
Let me know your feedbacks on that