By Design:
On windows resolution is stored in the registry under keys such as "Software/<Company Name>/<Project Name>/Screenmanager Resolution Width"
If the resolution is specified in the registry, the "Default is Native Resolution" option will be ignored.
The registry key was probably set from a previous run of the game using the resolution dialog before the "Default is Native Resolution" was set.
This is expected behavior

Steps to reproduce:
1. Create a new project
2. Make sure that "Default is Native resolution" is checked
3. Make sure that "Default is Fullscreen" is checked
4. Disable the Resolution dialog
5. Build for standalone
6. Run the build

Expected result: build resolution is whatever the native resolution is
Actual result: build resolution is 1024x768

Reproduced on 5.6.0p1, 5.6.0p3, 5.6.1p1, 2017.1.0b6*
Not reproduced on 5.6.0f3
Regression introduced in 5.6.0p1

VERIFIED FIXED 2017.1.3p4, 2017.2.3f1, 2017.4.3f1, 2018.1.2f1

Notes:
-Even after disabling "Default is Native resolution", changing values and then enabling again, the bug stays.
*-2017.1.0b6 "Default is fullscreen" also does not become fullscreen by default

trunk PR: https://ono.unity3d.com/unity/unity/pull-request/51270/_/platform/windows/default-screen-resolution-bug