Have the good folks at DO considered extending the tentacles of this marvelous software into the windows save as (or open for that matter) dialog box? For instance I make copious use of folder aliases. Being able to type in an alias here would make me very happy...
BTW notice the blank column to the LHS of the screenshot. That is like that since I installed DO. It should have some std buttons to take you to locations such as My Docs etc. I have never bothered to try and fix it... It is a mouse function and I hate using a mouse.
I doubt that the blank column on the left is due to Opus. The paths in that column are defined by registry settings which Opus doesn't read or write (or know about at all essentially).
Looks like you're using XP, so grab TweakUI from Microsoft's website and see what it thinks the paths are set to (if anything). TweakUI also lets you edit/define the paths so it should be able to fix the problem.
(On Vista there's no need for TweakUI as you can drag & drop items to the bar on the left.)