What are you doing to manage the transaction log? If your database is in Full recovery mode you should have a job that performs a transaction log backup.
Also would you consider just rebuilding the indexes on those fragmented indexes > than some percent of fragmentation?
Just some random thoughts here.
Good luck.
Kurt
Kurt W. Zimmerman
SR DBA
Lefrak Organization
New York, NY
http://www.linkedin.com/in/kurtwzimmerman