Symptoms
The Virtual Machine (VM) window is not visible after upgrade from Mac OS X Snow Leopard to Mac OS X Lion while the live screenshot in the Dock
and in the VM list 
indicates that the VM is running.
Cause
Parallels Desktop for Mac 6 was running in another space prior to the Mac OS upgrade to Lion.Resolution
Please perform the following steps:
1) Go to Applications on the Mac side and start Mission Control app:
2) Delete all spaces.
To delete a space you can hold the ALT button and press the cross.
3) Restart Parallels Desktop
4) Start the Virtual Machine
Add removed Spaces if you like. The Virtual Machine window will appear in the 1st space.