I installed SS on my iMac running Mail in High Sierra – it is set up properly and Junk Mail is turned off = but the Junk filter is working still [sometimes] and SS works too - I just want to use SS but junk mail still operates - thanks - this is not happening on my MacBook Pro [don’t recall but think I haven’t updated beyond Sierra yet]
It looks like Mail’s junk filter is off, but the iCloud server junk filter is still operating (because it can’t be turned off). For more information, please see this page.