If you uncheck an Advance Option and it appears to come back the next time you open the popup, the cause is almost always the same two-part behaviour: the checkbox state is saved per URL, and the change only takes effect once you click Save.
In other words, Auto Refresh is not ignoring your click — it is showing you the saved state for the URL that is currently active in the popup. Once you understand the per-URL model, the "ghost checkbox" goes away.
Switch to the tab whose URL you want to update first. The popup reads its settings from the URL currently shown in the URL field, so opening it from a different tab will show that tab's saved state instead.

In Advance Options, uncheck the checkbox you want disabled. The change is only kept after a Save click — closing the popup before saving will discard the change and the checkbox will look "re-enabled" the next time you open it.

Refresh only on current tab
Stop after 3 number of auto refresh
Show visual timer on the webpage
Stop refreshing if click anywhere on the page
Hard Refresh
By default, all Advance Options are disabled. But the moment you enable one on a URL, Auto Refresh stores that preference against that specific URL. The next time you open the popup on a different URL, you see the default state again — which can look like the checkbox is "re-enabling itself".
If a setting still appears to come back after Save on the same URL, send us the URL pattern and a short screen recording — there are a couple of edge cases involving very long or fragmented URLs we can verify directly.