I had this issue after upgrading to the new iPhoto. Heres what AppleCare phone support told me and it worked:
1) Confim that all of your Contact, Calenders, and Notes are in iCloud by going to iCloud.com
2) Once confimed, go to System Prefrences. Select iCloud.
3) Sign Out of iCloud.
4) When it asks you if you want to keep all your iCloud data on you Mac, select no to all of them. When you turn it back on, if the data is in your computer and iCloud, it will double up.
5) Restart your computer
6) When you have returned to your desktop, go back into System Prefrences>iCloud.
7) Sign back in
This is what an advisor at AppleCare told me and it worked for me and a friend.