Apinaud, as far as I know, that feature has always been "Due Soon or Flagged"; I don't know of a time where it's been possible to set it to "Overdue or Flagged".
If you reinstall OmniFocus 1.6.1 from
this link, can you send a screenshot of what you were seeing in the old version of the application to the
Support Ninjas? That will help us suggest what needs to be adjusted in v1.7...
(You can take a screenshot by pressing command-shift-4, which will give you a selection cursor. Tap your Space key, click on the window you want to capture, and when you release the mouse the image will be saved to your desktop as 'Picture 1', 'Picture 2', etc.)
You can then drag the images to an email message and send them to us. We'll use the information they contain to try and figure out what's going on here.