Figure I should share my fix here since I've been using switchmon for over a few years now. I myself use an Xbox One controller and originally had the same issue with Controller not working in...
If you have trouble getting SwitchMon to work, here's something to try. I had an issue where pressing the assigned button would switch to a FFXI window only if I was in a non FFXI window, and then wouldn't switch to the other FFXI window at all. If you're having a similar issue, try this:
First, if SwitchMon doesn't see the game windows at all, download the version on the downloads page. (credit for finding this info goes to this post).
Then, download a tool called XInput Plus. Download link here.
Now, we will patch the Switchmon .exe with this tool. Launch XInput Plus. At the top of the window is a text box called "Target Program".
Click on Select, then browse to where you saved SwitchMon. Once in the correct folder, select "FFOSwitchMon" and click on open.
Next click on the "DirectInput" tab and tick the box "Enable DirectInput Output".
Now, go to the "Settings" tab, then click on the Dll Files tab.
In the "Installed Files" section, tick the boxes of all the .dll files.
Finally, click on "Apply" and apply the settings to the .exe.
SwitchMon should now work, and switch between the FFXI windows when your assigned button is pressed.
Note: If it is still not working, try running SwitchMon in Windows XP Service Pack 3 compatibility mode.