For those still having this issue it seems that the culprit appears to be the option called "Use Dx11" in the Player Settings. Disabling this completely fixed the issue for me. I am using Unity 4.6 but since others are still having this issue in much later versions I am posting the solution that worked for me.

Disabling the setting now enables perfect raycast input detection at ANY resolution windowed or fullscreen.

The use of Dx11 appears to make the scaling in Unity completely go weird, disabling Dx11 allows much better scaling of the game too which is noticeable in the exe build.

Same issue here.....

It is most unfortunate that this issue is marked closed so it cannot be voted on. What is the most recent statement from Unity3D development team regarding this issue?

I just upgraded to Unity 5.3.4, and am STILL experiencing this issue. It is not just in 5.1 and 5.2. I have been searching the internet far and wide for some sort of resolution, but thus far, have not found anything. Do I have to go back and install those Unity3D versions to get the patch? If so, it seems that it would have been included in future patches as well. I cannot finish my product without a resolution to this. Literally. I cannot get the resolution onto the Surface Pro 4 screen, even starting from scratch and building the project on the Surface Pro 4.

What is the status of this? If fixed, would like to know what steps to take to experience that fix.

I have problems with some buttons on my 2nd scene, but not in the first. One important differance between the scenes is that in the first scene I add the buttons from the start, but in the second I add them after a while. In the first scene they are far to the left on screen, in the second they are close to the middle. If I click a bit to the right of the buttons in the scene where they are not working, I pop out of fullscreen mode.

Unity Version is 5.3.0f4.

Same issue here!

Same issue for me... :-(

There's also this issue

http://issuetracker.unity3d.com/issues/standalone-inconsistent-direct3d-behavior-with-non-native-resolution-on-fullscreen-builds

which I believe is related.

The 5.1.3 patch 3 from 11 September should include a fix for that:

(722983) - Fixed broken positioning of render when upscaling to native desktop resolution in full screen mode (Direct3D 9 and Direct3D 11).

But for example a 4:3 game is still stretched to fit a 16:10 desktop resolution in D3D11 full screen mode and the mouse position is still incorrect. It seems nothing has changed in that regard.

Same issue here. NOT fixed in 5.2 despite the "Duplicate issue" claiming its fixed.

Same problem on Unity 5.2.
I use NGUI for my project, and you ?

Same problem here, with Unity 5.1.2f1.