I have 2 windows open - graphic editor and the mixer but this actually works with any combination.
If I quit and relaunch metro they are both there.
If I put one of then in the dock, quit and relaunch metro they are both still there.
If I put them both in the dock and quit and relaunch metro they are nowhere to be seen. This seems to happen if I have 4-5 windows open and they're all in the dock.
The transport window is on "float" if that's an issue.
In fact if I turn it off and save preferences it comes back floating again.
Does it always float now? (unless closed )
scoot.