I have VMM 2012 SP1 (Upgraded from RTM) Managing a 7 Node 2008 R2 SP1 Cluster, all at WMF 3.0 with Hyper-V hotfix. I use Powershell, VMM and Excel to create reports on storage and memory consumption for an assortment of clouds/tenants.
I recently added a pre-exisiting virtual machine to VMM that had 2 Dynamicaly Expanding VHDs that both had space available to compact. After migrating it to the cluster (prior to compacting) the full size of the VHDs was displayed (~300GB). I ran a compact and the total size and acording to Windows Exporer it went from 300 GB to about 120GB, but in VMM it remained at 300GB. I refreshed, migrated, restarted, recompacted, waited over 24 hours and nothing changed and there are no errors in my job logs, but the size remained at ~300GB. What finally fixed it was creating a checkpoint and immediately removing the checkpoint. Then I realised that no Virtual machines are updating their size, or have been updating their size since the upgrade. I have another VM that shows 0.01 GB used in VMM when in Windows Explorer it shows 109GB. another that shows 730GB but is now actually at 780GB. So creating and removing checkpoints for 200+ running virtual machines is not an option.
This means quotas aren't being enforced properly and my reports arent acurate, which is incredibly bad for me.
In VMM2012 RTM this wasnt a problem as numbers would change at least on a daily basis, which is my reporting period. Now, the storage numbers on my reports barely change.