This is likely caused by the website creating more items after this addon cleared the selected items. I created a "Close tab" option in version 1.4.0 to prevent that, does that fix it for you?

Update: paint.net redirects to warrenpaint.com. This addon will only clear data for the current domain, so paint.net items will remain untouched. Maybe in the future I will add an option for specifying domains manually or including any host names found in the source of the current page.