I had the same problem with the Inbox refresh, and found the solution here: http://groups.google.com/group/Google-Desktop_Something-Broken/browse_thread/thread/7e982af0e9d1e2b8

Dan

1. Click File -> New -> Search Folder
2. In the New Search Folder window, scroll down to the bottom and select Create a custom search folder
3. Click Choose
4. Type a name for your folder
5. Click Criteria
6. Click More Choices
7. Assign to a category if you choose
8. Click the check box next to Only items that are:
9. Select Unread from the drop down menu
10. Click OK and you will be returned to the Custom Search Folder window
11. Now click Browse
12. Clear the Personal Folders check box
13. Check the RSS feeds check box
13. Make sure the Search subfolders check box is checked also!
14. Click OK
15. Click OK again
16. Click OK one more time!

You should now have a new search folder that identifies just your new RSS feeds. To make finding them easier, consider adding the search folder to your Favorites by right-clicking your new Search Folder and selecting Add to Favorite Folders.

Enjoy!

Work-around:
Create a new searhc folder. Add all unread items in folder InBox wih RSS = “” and you have a new UNREAD WITH NO RSS