I am on a Mac Pro with Magic Trackpad. Using Photoshop CS5, the cursor/pointer disappears after a while, and I have to switch to another application, then back to Photoshop to bring it back. The pointer does not disappear over the image window, just over the tool palettes, toolbar, menus, etc. This is a recent development, and I've only ever seen it in Mountain Lion. None of my previous systems exhibited this behavior.
This is a known problem with Mountain Lion. Do a search for this and see if there is any workaround.
Thank you Curt. I didn't see your answer until today, because this stupid forum is still failing to deliver my email notifications.