I too was having this issue, and it was VxxxxC's answer that led to the solution for me. I use a pointer utility, KeyMou, (from Many Tricks) to highlight the pointer to improve visibility. Turning KeyMou off resolved the issue.
Update: In further investigation, along with the support staff at Many Tricks, it seems that it is a combination of utilities that is causing my issue. In my case if both KeyMou and PopClip are enabled, the issue presents. If either (or both) are disabled, the issue is resolved.
So while the OP doesn't say anything about using such a utility I doubt it is a coincidence that the issue appears when such a utility is in use and disappears when it is not.