Comment 1 for bug 1459996

This happens to me too. I notice it particularly when hovering over links, tabs, and "close tab" icons. Interestingly in the case of the latter, the cursor does not disappear until the "Close tab" tooltip appears. So perhaps there is some sort of conflict between them.

This issue has been discussed on the forum: see https://www.raspberrypi.org/forums/viewtopic.php?f=28&t=86135&p=778497 . A "fix" suggested in this discussion is to delete or rename /usr/share/icons/Adwaita. This does work, but is obviously kludgy and results in not being able to tell when the program you've selected is starting up, because the mouse cursor with the little wheel is gone.

I find it especially problematic when trying to select in GIMP. It's very difficult to select just what you want when your cursor is disappearing on you.