I'm glad you are enjoying the mods, at least!
Yes, it's a common issue, unfortunately. Isolated the saves helps a bit, but mistakes can still happen. The problem is not knowing which save belongs to which mod, since there's no unique finger print for each mod in the environment. The mods do have a mods.xml, but you can have multiple ones, such as Valmod + SMX, so it's not unique enough. The Mod Launcher may have to make its own unique id for each mod, and try to help save them.