On starting the CUI command you may receive alerts about unresolved files that can no longer be found. To clean these up, expand the ‘Partial Customization Files’ section and look along the list for items with an (Unresolved) suffix. If you can’t resolve the item, right click and choose ‘Unload’.
Sometimes viewports imported (DesignCenter, etc) don’t display the contents, etc. Issue the MVIEW command, use the ON option, and select the misbehaving viewports.