Hi,
I also have this issue. It was very weird. The mouse will freeze every time you move to a new window or application. In fact it is no just the move. If you cmd-tab to switch apps then it won't work, keep tapping the keys and you will know when it is back working. I used this method to quit apps thinking once I quit one of them it will all return. Nothing changed. Once I quit all the apps I started on the "hidden apps". As soon as I quit BTT it all came back. Immediately reopen and all is good again.
I have a Magic Trackpad 2 and also run Bartender. I also use a lot of Desktops over two monitors. I am running 10.13.5. If there is any information I can provide, I am more than happy to do so.