Thanks for the suggestions. I should have said I'm running the Nouveau driver and the displays are set up to act as a single desktop using the "Monitor Preferences" utility that's bundled with LMDE/MATE. I've done this for years using the closed nvidia driver and twinview, as you described, with lots of other desktop environments, and it's always been fine. The current driver configuration works fine under Cinnamon.
Unfortunately, even the "Show windows of all workspaces" setting doesn't help. It still ignores windows in the upper display/half of the desktop. When I drag a window from upper to lower, it appears on the list, then disappears as it's dragged back up. MATE's Window Selector app (the one that pops up a menu of available windows, rather than displaying buttons) shows everything, but the Window List app only seems to see the half of the desktop where the panel is actually located.
EDIT: It turns out that there were several instances of window list running, with all but one being hidden while the panel "Expand" property was active. Disabling Expand, I could delete all the instances, add one back in, and set the Expand property again. All is now working as it should.