For anyone else finding this: I've seen the same issue on latest factorio and helmod versions, and for me it only happened in a certain seablock modpack savegame that I started around ~0.18.22. For some time now, in that save the panel has always been on screen like in the screenshot above. Opening and closing helmod using the U hotkey didn't help. It also didn't help to disable the properties window in mod settings, even when saving the game and reloading that save, the window stayed visible.
The only way I found to get rid of the window permanently was to remove all helmod data from the save. As a warning, this will include not only the settings, but also the plannings you made in helmod. Mine were a mess anyway ;)
steps to fix broken save by removing all helmod data:
- save your game
- quit to main menu, remove helmod from loaded mods and restart
- load and save your game once without helmod active
- quit to main menu, enable helmod again, restart once more