How to reproduce:
1. Create a new project
2. Import the ProBuilder package from the Package Manager
3. Open the Scene view or the Game view (Window -> General -> Scene/Game)
4. Click the Gizmos button in the Scene/Game toolbar to view the Gizmos menu
5. Hide all of the icons
6. Close and reopen the Editor
7. Open the Gizmos menu again

Expected result: all of the icons remain hidden
Actual result: some of the icons are hidden, some are shown

Reproducible with: 2019.1.0a14, 2019.4.13f1, 2020.1.11f1, 2020.2.0b8, 2021.1.0a2 (4.4.0)
Not reproducible with: 2018.4.29f1 (3.0.0, 4.4.0), 2019.1.0a13 (3.0.0)

Notes:
After reopening the Editor in 2020.1.11f1, 2020.2.0b8, 2021.1.0a2 most of the icons are no longer displayed in the Gizmos menu. After removing the ProBuilder package the icons reappear and some of them reset