I am getting this issue as well but I am not sure what's causing it. Sometimes I think it's the mousewheel scroll to move the screen but then it doesn't happen at all.... Cursor comes back into visibility after leaving the game window and coming back.
Thanks for the report. I really need to see game logs and system specs before I can look further into this. If you could send something through to the address listed under the "Technical help" section here on the store page, I'll be happy to look into it.