Hope I'm not being over-simplistic, but it sounds like you need to go to your View menu and choose Sidebar Options > Show Note Counts. Perhaps this option got deselected when you did the upgrade. If this is not the case I apologise for the suggestion. Yup. Whoops. Not over-simplistic. Here's the thing, though I searched FOREVER to find out if this was just some option that had turned off and couldn't find anything about it anywhere. Thank you for your help.
One MAJOR issue for me is that my note counts aren't displaying next to my tag list. This is an absolute productivity-killer for me. Not happy at all right now.