This is strange. I right-click on a track in Console View and select Hide Track; The track disappears. As soon as I select another track, the hidden track reappears. I found that when I uncheck "keep track/console visibility states in sync", the problem goes away. Is this a bug or am I missing something?

I've had similar inconsistencies in X3 opening project originally made in Sonar 4 or 8.
Even in track manager dialog unchecking sync - you see sometimes that track view status is coming up opening from console.
 
Now running 2015 I see track manager is the same - the focus you have opening it decide where it applies, which is difficult sometimes to know, like when really in Inspector etc.
 
A simple matrix like most managers use would be better I think. A column for visibility in track and console view - just check where it is to be visible.
 
Sorry, have no solution for you, just possibles clues that i might be a bug...

It's never been inconsistent for me.  Essentially it never works from the console view.
 
D (as a shortcut) is a great friend.  One key stroke and you're back to track view, where you can click H to get to the Track Manager, make your selections, and click D again and you're back at the Console view.  No biggee.
 
What is a huge time saver for the Console view though is selecting what tracks you want to show by type.  So if you indicate you don't want to show Muted tracks, for example, you can save a lot of wasted real estate automatically.  (Even though those tracks show in the Track view, they wont' show in the Console view if you've opted out of Muted tracks for the Console view in that example).

Maybe it's better with two dialogs - track manager and console manager - and each have it's own keyboard shortcut.
 
But I miss simplicity of just a column for each to change in both views.
Don't feel the need for tree view - unless there really is a tree for a folder in console view as well, as Reaper does it.

Thanks for the responses, guys. So, I tried it in another project and it works. Now I'm really confused. LOL