SQL 2005 64bit and R98404

So I decided to run R98404 across my entire database (following the OTI to have all of the tables listed in F9843) and it only generated the primary keys! I checked the sysindexes view in the database and the names of the indexes are still in there.

Anyone ever see this issue and know how to correct it? I reran R98404 for only 1 table and got the same results.

Misread the new interface in Enterprise Manager. They have a new folder for indexes, I was just looking in the "Keys" folder.

Either way, the indexes for F0911 did not create so I am rerunning that one to see if the job will work for just that table.