17.10 gnome icons don't reflect/use existing open windows in certain applications

In Ubuntu 17.10 using ubuntu or gnome desktop, certain application icons do not work properly. Specifically unpinned apps don't appear in Docky (gedit), once launched, open app indicator icons do not appear (gedit, libreoffice writer, calc, GIMP). If one of these applications is opened, clicking on the icon in docky launches a new instance rather than switching to an existing instance. Changing back to unity desktop resolves the issue.

I attempted several workarounds, including deleting and readding icons to dock, uninstalling and reinstalling Docky. No luck with any. Verified on four other computers from different manufacturers. Consistent problem that appears to be application-specific. For example, Firefox appears to work properly.