Hi r2d3, i can verify the issue with New Window in Sierra, but its relatively easy to fix.

- Right click on Moi V3.1.app and select Show Package Contents.
- Navigate to folder: Contents / Resources / WineskinMenuScripts

In the WineskinMenuScripts folder you'll see a file called NewWindow.app which looks like:


Right click on that and choose open, then open with Automator.
Inside Automator choose save, overwriting the original file and then quit Automator.

Thats it! New window should work fine after that.