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The scrollbar-over-the-right-side-contents is a system-wide issue. It's really for Apple to fix, not Omni (afaict). Of course, if Apple doesn't fix it (and they may have I haven't jumped into Mavericks yet), Omni might consider changing how they use that right-most space of the window.

I try to remember to use the "Show/Hide Note" keyboard shortcut: ⌘'