Photo stream only keeps photos in iCloud for 30 days, even though it will keep up to 1000 photos on your devices until they are deleted. When you enabled photo stream on your PC you would only receive photos added to photo stream from the last 30 days (as the others are no longer in iCloud).
If you want to transfer the remaining photos to your PC, save them to the camera roll on your phone (if not already there) by tapping Edit, tap the photos, tap Share, tap Save to Camera Roll. Then import them to your PC as explained in this article: http://support.apple.com/kb/HT4083.