Reproduction steps:
1. Create a new Unity project.
2. Go to File > Build Settings > Player Settings.
3. Set D3D9 and D3D11 Fullscreen Modes to Exclusive Mode.
4. Build a Windows standalone using Direct3D11.
5. Swap between fullscreen modes with alt + enter.
6. Notice, that editor goes to the other monitor when entering full screen mode and to the middle between monitors when leaving it.
7. Build a Windows standalone using Direct3D9.
8. Make sure editor is in the full screen mode.
9. Repeat step 5 and notice, that editor goes to the middle between screens when entering full screen mode and to the other monitor when leaving it.

Workaround:
Build with "FullScreen window" Fullscreen Mode.

Note:
Case 611200 might be related to this one.