[nixsee]

One bug (x64 version)

1. I made some highlights and notes.
2. Then I changed the color of the reader from Black to White (to see if the highlight colors that I mentioned in my above comment were more pleasing). No highlights were displayed, but the references were still shown in the Highlight Browser.
3. Switched back to Black and no highlights were presented despite being in the browser.
4. Created new highlight and all previous highlights disappeared altogether from the browser.
5. Closed and reopened the book - now many highlights are showing in both the viewer and the browser. I'll have to clear them all out and create new ones in both Black and White modes to see which ones are being saved and displayed after close/open.
** On that note, it would be nice if there was either multi-select (Ctrl and/or Shift Click, Shift+Arrow Keys) option in the highlight browser, as well as ability to bulk edit/delete them. Also allowing to use the Delete key would be helpful to avoid many clicks)

Follow-up:
I created a couple in Black, then a couple in White, closed and reopened. All 4 were in the browser with their notes stored, but the 2nd highlight from Black was not being displayed in the viewer.