You downloaded an iCloud backup to your PC? I assume you mean you downloaded your photo stream to your PC. What you may not know is that photo stream only keeps your photos for 30 days. After that, they are deleted from photo stream but not from any device that already has them (such as your phone). When you enabled photo stream on your PC you only had access to photos from the last 30 days since the others are no longer there, even though they remain on your phone.
To transfer these to your computer at this point you have two options:
- Save them to the camera roll on your phone (by opening the my photo stream album, tap Edit, tap all the photos, tap Share, tap Save to Camera Roll. (You can only import photos to your computer from the Camera Roll album.) Then import them to your computer as described here: http://support.apple.com/kb/HT4083; or
- Use an app like PhotoSync, which can wirelessly transfer photos from any album between your devices/computers, including the my photo stream album.
In the future, always import your photos from your camera roll to your computer via USB before deleting them. Don't rely on photo stream or your iCloud backup to save your photos.