Where can I go in SkinStudio to fix this problem?
You ask this question than you say "Editing the Tree view and explorer sections did not help"
So you are saying you already checked the treeview section in SS. So in SS EditControls/Treeview section the Tooltips/ Background is the mouse over image. However if you need to change the left side color that would be in the Edit Explorer/IE shall parts go to the folders bar. Than to Extra Settings and change the color. Note you must have an image in there. It can be a stock image but one must be in there.
If that isn't what you are looking for a screen shot would help.