Repro steps:

1. Open "ReproProject" project
2. Build for Windows Standalone through the build settings
3. See that the project finishes building (with some errors)
4. Restart Unity
5. Build the project by "Build and Run"

Expected result: The project should build exactly as the one with the "Build" Option
Actual result: The building of the project fails with errors ("Error building Player: 2 errors")

Reproduced with: 2017.2.0b1, 2017.1.0f1, 5.6.2f1, 5.5.3p4, 5.5.3p3
Regression introduced in: 5.5.3p3
Did not reproduce on: 5.5.0f3, 5.5.2p3, 5.5.3f1, 5.5.3p1, 5.5.3p2,

Note:
If you first build the project with the "Build" option and, without restarting Unity, you build with "Build and Run" the errors don't appear and the build finishes successfully