This is just wierd. I have 7 boards in my favorites list. When I view the list on my favorites page, 4 have x's to remove them from the list, the others don't. Those that do will show up when I view by the scope "favorites" (assuming all 7 have changed), the others won't. None seem to show up reliably using "changed since last login". Sometimes the list looks right, sometimes it shows no messages. This is 15 seconds after I just changed (replied to) a message. Occasionally, simply refreshing the view will fix it. The "bold if changed since last login" idea also doesn't appear to work properly though it could be due to the "changed since last login" problem.
Boards that have x's:
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Boards that don't:
The last two are obviously private boards, maybe that has something to do with it...