Photo stream photos only remain in iCloud for 30 days, even though your last 1000 remain on your phone until deleted. As a result, when you first enable photo stream you only get photos from the last 30 days.
To stream old photos to your PC, add them to a shared stream on your phone and invite yourself as a subscriber, as explained here: http://help.apple.com/icloud/#/mmc0cd7e99. Or, you can transfer them to your PC of your wifi using an app like PhotoSync.