Had this problem too: I just came home from a trip and sat down to email all of my photos from the weekend to friends. Surprise. Only three of the photos had synced to Photo Stream on my iPhone so those were the only ones showing up in iPhoto on my mac. I waited for a minute to see if iPhoto would update the rest, but no. When I looked on my iPhone I saw it was because only those three photos showed up under photo stream, but all of the photos showed up on the camera roll.
Semi-solution but not really: I went to "settings" on my phone and then "iCloud" settings. Suddenly, without me doing anything, it just started saying "upgrading" and the rest of the pictures slowly started showing up in Photo Stream on my phone. It looks like they are very slowly being added to iPhoto on my mac now, but the phone settings still says iCloud is "upgrading". I do not know what this is about. It seems that iCloud should automatically upgrade. Not sure why it didn't until just now when I opened settings or why it is taking so long, but maybe this will help someone? It's a brand new iPhone with plenty of space. I also have space on iCloud.