Hi!
It happens, because there is a separately configurable limit for the initial page load (auto-populate), as well as the regular results.
I am guessing, that for the auto-populate you have a higher limit set, but for the regular results it is only set to the default 10. Once a filter is checked/unchecked, it is no longer considered as auto populate.
You can change the regular results limit under the General Options -> Limits panel: https://i.imgur.com/64Xtcir.png
..and the auto-populate limit under the Layout Options -> Results layout panel: https://i.imgur.com/Kuy0hhr.png
Changing them both to the same number will do the trick.