In general it's a good idea to look in activity monitor for processes that take a lot of CPU when they shouldn't. (Such issues appear when the system is not able to process the event queue fast enough, this usually happens when multiple apps access the event queue or when something is taking up all the CPU).
Do you have other keyboard or mouse related apps installed?
Upgrading to 10.14.4 doesn't appear to have solved the issue. I did have some touchbar customization, but I've since disabled "Enable Touchbar Support" to see if that would clear the issue. It has not.
Then I'm a bit out of ideas. It could be all sorts of conflicts with other apps but these can be hard to track down.
Maybe go to the about view and click the "Export Debug Information" button. This will create a folder called BetterTouchToolDebug on your Desktop that you can send to firstname.lastname@example.org, then I can check the logs. (Unfortunately in such cases there often is no unusual logs though).
You could also send me a list of the currently running processes from Activity Monitor (just cmd+a and cmd+c to copy the whole list in Activity Monitor).