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"Compacting Virtual Disk(s)" on every backup

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Our backups on our virtual windows server 2012 R2 which is hosted on Hyper-V server 2012 R2 have been taking at least 3 hours longer than they used to.
We use windows Server Backup for nightly backups which backs up to a local volume. We also use a powershell script for the weekly backup which also runs through wbadmin and backs up to a network share. 
A couple weeks ago the backups started taking 3-5 hours longer.  I monitored them and noticed that they have been taking hours to compact the virtual hard disks at the end of the backups.
I refereed to the following link about this process and it should not be happening for every backup.
http://support.microsoft.com/kb/2524602/en-us

We installed windows updates after this problem began but its is still happening for every backup.

What can we do to stop this?




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