A few years back, I had a client that was having some performance issues with an application. A colleague of mine and I isolated a poorly performing database instance in their staging environment as one of the causes.
Their production environment was using a Sql Server 2000 instance with a database that had been around for 4 or 5 years; their staging database server was running Sql Server 2005 on which a backup of their production database was restored. Our testing showed the staging server was consistently performing significantly worse than production.
We eliminated hardware differences by installing instances of Sql Server 2000 and 2005 on a new machine and restoring the same backup to both. Having verified that a similar performance disparity existed between the instances on the new machine, we performed consistency checks and rebuilt indexes to no effect. We found that creating a new database in the 2005 instance with an identical schema and migrating only the data eliminated the performance disparity. Based on circumstances, we decided there was no need to pursue the issue further.