Hi there,
I’m now trying to implement audio plugin using JUCE 1.20 and JuceAudioPlugin v1.3.
Although basically it uses window group, it causes some problem.
One is the window activation. When I click VST window content, the base window which owned by host app is not activated but the content window is activated.
The other issue is window minimizing(collapsing). When the window is collapsed, the content window is hidden, only the base window which is filled with white color is collapsed.
This is not Juce specific thing, I found the similar behavior in Digital Performer v4.1.x (earlier than v4.5). It had a problem with collapse. But in the latest version, it was fixed. DP also uses window group for plugin window. When the window is collapsed, it seems that DP hides the content window and maybe capture window content and draws it into base window with transparent white, then collapses it. So the minimized picture can be shown in the dock. This may be one of good workaround.
It is hard to implement VST GUI on Mac OS X… (This is one of the reason I’m trying to use Juce) There are old architecture based host and modern architecture host… We still have to consider non-carbon event based host app like CubaseLE v1.x or carbon event based, and non-composite or composite… and QD functions are now deprecated… 
Best regards,
Masanao Hayashi
Korg Inc.