We've just released a new DisplayFusion beta version (http://www.displayfusion.com/Download/Beta/) and most of the Start menu issues should be fixed up now. For setups where font/DPI scaling is not used, the Start menu will open directly on whatever monitor you clicked the Start button on. For setups where the non-Primary monitors have different DPI scaling settings, the Start menu will open on the Primary monitor, then move to the monitor you clicked the Start button on.
Please let us know if you run into any trouble after updating.