I do still have both the maps and savegames folder; neither is empty, at it happens. I agree, the mod launcher is perfect for keeping the savegames separate, especially when using incompatible mods.
At the moment, I don't remember which folders I deleted.
If I encounter the problem again when I install the soon-to-be-released update, I'll report back.
One other item of potential interest that I haven't seen mentioned; not a bug, just a quirk: If the player or AI produces colonizers in a system that happens to have random movement of ships, the colonizers will start off-planet. Any automated command, either by the AI or the player using the "send colonizer" button, that activates those colonizers will fail to load colonists and result in the creation of zero-population colonists which then have to be manually populated, as the transport minister never seems to do so, in my experience.