Does your splash screen remember your last checked items?

[Meneth]

The real cause is that some mods use a custom temp folder. So the checked mods get saved there.
Then, the launcher reads the vanilla settings file, and thus doesn't see anything checked.

A fix of sorts is simply overwriting the vanilla settings file with the mod's settings file. You'll get the same items checked then as the last time you launched that mod.

 

[Meneth]

Interesting.
I didnt think of that.
I have my own general user directory anway and delete the user_dir lines for the mods that do so.
Though in my experience the mods without own user directories and with spaces in between words didn't stick as well.
Ah well.

Yeah, the spaces are a separate issue.