I seem to have the same issue, under ubuntu 12.04 64-bit.
even after closing and reopening ST3 doesnt make the files appear...
ST3 is pretty unusable for me at this moment
edit: ok, i just noticed something weird... when I click to open a folder and then RESIZE the sidebar, the files show up, sort of, but it renders them badly.
This looks like a platform specific graphical issue within ST3? (note that previous version of ST3 didnt have this problem and my ST2 that is still installed, works ok)