Update - replacement signature cover made no difference. I've also tried the latest advice in this thread. Cleaning contacts and removing/uninistalling cover drivers/filters has made no difference. I now have the signature cover on my Surface Pro 3 (i7) where the hesitation is slight, with the old Pro 3 cover on the Surface Pro 6, which seems to work fine.
The hesitation is simple to recreate. Just continually circle the cursor using touchpad and eventually it will lose focus - the cursor stops and you have to lift the finger to reengage.
I am reluctant to try replacing the Pro 6 as I don't want to have to reconfigure a new one. I've tried running in safe/restricted mode with all non-MS software/drivers diabled - no difference.