Hello,
The sense of Modality mode is that you see your virtual machine transparent while you are running some Mac applications. When the machine's window is active - it is full opaque. Now, just click on some Mac window to make it active and you will still see the machine, but as transparent as you have configured.
So, to sum up - Modality window becomes transparent when it is inactive (btw, that's exactly what happens when Configuration is opened)