I just experienced this same issue, for the first time, while I had a window open, on the CBS website, watching an episode of NCIS. This manifested itself, when I opened a new window, to do something, in the newly opened window, while the show NCIS was playing in the open window underneath.
Bringing up a new window, in order to search this issue, I was able to experience this disappearing cursor on multiple occasions, during the "show".
When finished with watching the NCIS episode, leaving the CBS website, the disappearing cursor issue also stopped.
Running MAC OS/X 10.6.8, Safari Version 5.1.2 (6534.52.7), all updates current as of this date, Macbook Pro 13".
Model Name: MacBook Pro
Model Identifier: MacBookPro8,1
Processor Name: Intel Core i7
Processor Speed: 2.7 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Memory: 8 GB
Sudden Motion Sensor:
Hope this post proves helpful to others looking into this issue.
I have the same problem - will try re-installing Flash. But the quick way to get your cursor back is to run it up to a corner (I know, you can't see it, but...) that has Mission Control enabled (Preferences>Mission Control>Hot Corners...). All your windows will be exposéd.. just click back on the Safari window you were using.