Most likely these disks have had files on them that have been deleted. If so, now even though the quest OS is no longer maintaining pointers to the files they are still present on the disks (just like if you were dealing with a physical hard drive). Basic compression removes the "white space" as the backup copy of the disk is created. Basically creating a thin-provisioned clone. Since the free space, as reported by the OS, is really no longer "white" it is maintained in the backup copy.
We have not tested this yet, but you might look at SDelete from Sysinternals (http://technet.microsoft.com/en-us/sy...). By "re-zeroing" the unused space on the disk you might be able to get your backups to compress as they did before. Can you research and try this and let us know if it helps?
Just to be safe please be sure to make a good backup of your VM's before you try this or maybe try this on a restored clone.