I have a MBPr Late 2013, with 2 Dell 24" screens connected via Thunderbolt. I use only the external monitors, i.e., the MBPr is closed and the screen is turned off.
I have several VMs running, different versions of windows. I run some of them on full screen mode, with "all the displays enabled" option. There are times when switching between host' apps to the VM, or between VMs, when the focus returns to the VM the screens get incorrectly set: they are swapped in the Windows config and the host-secondary-screen (secondary for OS X, and originally secondary in Windows too) is changed to be the primary, the windows of the open apps "moved" and that display (in my case, is the one in the left) is set to the correct resolution (1920x1200) but shows a black bar on top and scales the VM screen to match the remaining space, which makes it look blurred That is solved enabling/disabling the "show menu bar" option in the View menu in Fusion.
I'm running Mavericks with all the available patches and updates applied. Fusion is version 6.0.2.
This doesn't happen always, and I haven't found a way to reproduce it 100% of the time. But this happens enough to be a real inconvenience.
On a related note: I tried to send this as a support request several weeks ago, and I only got a page telling me "Unable to complete your Request". I tried again today and got the same page.
Thanks in advance,
Rodrigo Gómez