Q: Trackpad gesture switching app not working

You may find that resetting the NVRAM will help.  here is Apple's document with instructions.

https://support.apple.com/en-gb/HT204063

Oh dear.     I'm reluctant to suggest resetting the SMC because, although it helps with many trackpad problems, gestures is not usually the case.     You could try re-setting the trackpad entirely rather than re-setting the one failing gesture  ...  but somehow I think you have been through this exercise.   I cannot believe that this could be an interference problem but just in case, have you introduced anything new into the environment like a phone hub or Wacom tablet? 

Have you been able to get this fixed?  I am having the same problem.

Cheers

I also noticed that when it pairs on the 10.11.6 that the magic mouse icon shows up.

I found this by searching around and it seems this person had the same issue as us.

http://apple.stackexchange.com/questions/213129/magic-mouse-2-and-magic-trackpad -2-are-recognized-as-mighty-mouse

I was able to fix mine by re-pairing.  So I turned off my magic trackpad 2 and then used my Macbook pro trackpad to remove the pairing from the bluetooth preferences.  Once it was removed, I just turned back on my magic trackpad 2 and this time it recognized it as a trackpad and not a magic mouse.

Hope that this works for you.

Cheers,

David