Continuous Protection Server (CPS) indexing takes longer in version 2010 R2/R3 than in previous versions.
Indexing in CPS 2010 R2/R3 is performed by Vivisimo and no longer by Autonomy as in previous versions. This step was necessary as indexing didn't perform as well as it was designed to.
Vivisimo indexing will take longer as it works differently and is more CPU and memory intensive.
Make sure that Indexing is located on a dedicated disk.
Make sure there is enough CPU power and memory available for the indexing process.