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The behavior is the same with mouse or keyboard. Also, it is the same for all checkboxes in any page, like the one of archlinux you shared. But I investigated more; I will re-explain the behavior. When I click on a checkbox (or hit the space button) I need to move the mouse to another checkbox so that the checkmark appear on the first. Also, similar anomaly happens when I press Ctrl+Tab to move to another tab. It requires me to move the mouse to the tab bar so that the new tab is selected.
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That sounds more like a general client bug/oddity - is it the same w/ all browsers? Does it actually behave different when not prime-run'ning the browser?
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Yes; it is with all browsers that I tried as I reported to you above. It only appears with prime-run
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