I've also experienced very frustrating issues with charging my pre-ordered Surface 3. The first couple weeks were fine. At night, I would watch a little Netflix in bed, shut off the screen, then plug it in to charge the next morning before I left for work.
A few weeks ago, I started noticing times where after being plugged in all day with the Microsoft power supply and cable (light on), the battery would have gained no charge. This is after sitting the entire day plugged in with the screen off.
This now seems to becoming more and more common. I've tried multiple cables with the Microsoft power supply and it is so inconsistent it is hard to pin down where the issue is. After the Surface 3 usb cable, I tried a Xbox One controller cable as well
as two standard micro usb cables. Sometimes, they'll say "Plugged in, charging" right away. Other times, they'll stay stuck on "Plugged in, not charging" until I unplug and replug things a few times. Today, using a micro usb cable I just purchased, I turned
the Surface on after being plugged in all night and the Surface did not even recognize that it was plugged in.
I'm still not sure if this is an issue with the power supply I received or with the Surface itself. The fact that this issue seems to occur with multiple cables including the one that came with the device leads me to believe that the cable is not the issue.
This is extremely frustrating to me. When I plug a device in with the screen off and the charge light comes on, I expect it to be charging. I do not want to have to manually check every single time I plug it in that it is, in fact, charging.
I'm considering returning the device based on this issue alone. I'm really disappointed since I enjoy working with the Surface a lot.
edit: I have also installed all Windows updates as of yesterday and this issue persisted.