There is a strangeness in Aperture which sometimes causes the filter on the Photos browser to get confused.
To check to see if this is your problem do:
- Select a smart folder in your library, anyone doesn't matter which.
- Open this smart folders Filter.
- Now without changing anything and leaving that filter box open select the Photos icon
- The name of the filter box will change to Smart Settings:Photos
- Look at the settings in this filter there should only be the Rating rule checked and it should be set to show all images (greater then or equal to X)
- If the filter has anything else set clear them all out and just have the rating set.
If this was your problem then the browser for the Photos should be back to showing all images.