I have Yoga 3 Pro, purchased about a year ago, and I have the same problem. Windows clearly has not corrected the problem. Using QuickBooks or my PDF converter program are agonizing (in desktop mode, which is where they reside). Even with my glasses, I have to lean into the laptop to see the menus. Even worse, I dialed into an online class and the chat room text was so small I was forced to use the magnifier to read the posts from class participants. I tried all of the scaling and resolution options in the settings, but the menus and icons remain tiny, even if all other text enlarges. I love my Yoga for lots of other reasons so I'm just putting up with it for now. Here is a good article about this problem. It refers to the Yoga 2, but applies to Yoga 3 as well. At least I know I'm not the only one.
http://arstechnica.com/gadgets/2014/03/lenovo-yoga-2-pro-review-you-say-you-want-resolution/2/