If you see prolonged startup time with Windows Server 2008 R2 servers with the Hyper-V role enabled, this can be caused by a large registry hive that increases after every backup.
“The issue occurs because of a large number of orphaned registry keys. The Volume Shadow Copy Service (VSS) snapshots create many registry keys. However, they are not deleted after the VSS snapshot operations are completed.”
The solution is hotfix KB982210: http://support.microsoft.com/kb/982210