This has come up a few times in the past...reported both my me and others for a while. This only seems to an issue on the mac.
When you go to fullscreen (via fullscreen 1 message to either jit.gl.window or now jit.gl.world) and small floating window appears at the bottom (see attached image). I get this about 30-40% of the time. For a while I thought it was an issue with my mbp (have seen it on many different flavors, including the most recent model), however we just finished development for a project and saw it on both several mac minis and new mac pros.
The work around has been either to use windows (where this issue doesn't exist) or to specify the rect for the window, and manually hide the menubar/cursor/etc. However using fullscreen msg is lovely if you find yourself developing for different different output resolutions (primarily 1920 x 1200 vs. 1920 x 1080) and don't want to fuss with changing the rect command (I know it's not a big deal...but still...).