I also have the same problem.
If I compact a VHD or VHDX the compact runs for one second and ends, and the VM's remain uncompacted.
I am using REFS format on the drive, and the VM's are Windows 7 x86, if that makes any difference.
I have disabled System Restore in VM's, as that was a known problem with 2008 R2.
Can this be reported as a bug in Server 2012 RC.