I clicked on the “Check for updates” button on the Updates page of NodeWorx and then decided not to run the InterWorx 6.1 update then. After a couple days it auto installed as expected, but when I went back to the updates page, those “pending” updates I brought up by clicking the button manually were still there. Click the button again cleared those out and replaced them with some new one for PHP.
Seems like it makes sense to clear that manual update list whenever the auto update is run to keep that display in sync.