Mac itunes trying to restore my iphone 6 plus

Both my Mac iTunes and iPhone 6 Plus are updated to the latest version. When I connect my iPhone via usb to my MBA, the Mac iTunes is asking to either set up my iPhone as new or restore from backup. The problem is the back up is only showing my iPad and iPad mini which probably I had them backup to the Mac instead of iCloud.
I would like to sync some content from the Mac to my iPhone but is not able to do so because of this. Btw the iPhone had been restored from my previous iPhone using iCloud backup which is under the same account as the iTunes (same username and password).
I have no problem backing up my photos and videos from the iPhone to the Mac using iPhoto.
How do I solve this problem? Thank you in advance.

Also having the problem. Phone ended up restoring to the last iTunes back up I'd made in October. Lost a few apps, texts and photos (also gone from photostream too) but music / playlists thankfully ok. Given up using iCloud for back up, decided to try to stick with iTunes again and see if that helps.

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