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After installing Panopoly with the Demo App I discovered that the pane content cache settings can't be accessed via the UI using the default Administration Theme (Responsive Bartik). I'm not sure if this is an issue with the way Page Manager is revealing this menu, or if it's a problem which should be fixed at the theme layer.
Using the default "Responsive Bartik" theme, the lower half of the pane settings menu is hidden behind Bartik's div#footer-wrapper.
I tried switching the admin theme to normal Bartik, and the menu overlapped the footer-wrapper, but was still truncated at the bottom of the screen (and unable to scroll up):
With Seven as the administration theme I was able to see and scroll down to the cache settings for the pane (as long as my cursor did not leave the menu).
For all three examples I was using Chrome 25.0.1364.160 for Mac OS 10.8.2. Screen Resolution 1440 × 900 (viewing Chrome in Full Screen Mode). I discovered this issue in 7.x-1.0-rc3 and confirmed that it was still an issue for 7.x-1.x-dev as of 9f43adbd.