I just upgraded to 4.1. I could have sworn in an earlier version that my Start button was on the left monitor (#1) and my system tray and clock and was to the far right of my second monitor (#2) which is how I would like it.

Currently my monitor on left has the Start button and then on the right side of the left monitor is the System tray.
Then my monitor on the right also has the system tray on its right side. Basically the system tray exist on the right side of both monitors.

Is there anyway to disable the system tray on the windows task bar but still have it show on the display fusion taskbar?

I disabled the system tray by editing the following in the registry HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Policies\Explorer
Created a DWORD called NoTrayItemsDisplay with a value of 1.

This unfortunletly disabled both the windows system tray on the left monitor (Good) AND the Displayfusion System Tray on the right monitor (Bad).

Any ideas?

Until somebody comes up with a better answer this work-around will put the systray on the right hand monitor only but unfortunately the start button on both.

Close DisplayFusion.
Right click on your taskbar and uncheck 'Lock Taskbar'.
Drag the taskbar to the right hand monitor.
Lock the taskbar.
Restart DisplayFusion.
Hide the clock and systray in the multi-monitor taskbar settings menu on your lefthand monitor.