I love the control + arrow to adjust all the track sizes to the same height.  However, I do not want my folder tracks to be the same size.  The are better off minimized as no editing can be done there.  It would be great to have an option to keep the folders minimized and only adjust the midi tracks.

I'm not seeing it. The folders remain minimized when I hit Ctrl + Up/Down arrow keys. Maybe there's a option somewhere. What version of Sonar are you using?