I tried everything here and this is what worked.
I first had to sync and transfer everything, then I rebooted my computer and my iPhone. I only had to do this once but I had to do it every time I wanted to backup to iTunes on my computer.
Even worse I was backing up because I was getting the new iPhone 6s and when I did the restore on the new iPhone I got the same message after 1 hour of restoring. After rebooting my computer, Instead of continuing my restore it had me upgrade to 9.0.1 which messed up everything because after all this I got the "hello" screen again and it started asking me how I wanted to restore. That sounds good but now the old backup I was using didn't show as available to restore. I decided to restore my iPhone which I thought would wipe out the 9.0.1 update but it just seamed to make it start over and gave me back access to the iphone6 backup. I plan to try to backup from this iPhone 6s tonight to see if this problem still happens.