I have noticed this too.
If I allow MO2 to "force enable game file" this does not include "ShateredSpace.esm" and "SFBGS004.esm" preventing LOOT from putting the mods in the right order. However even when I disable it, LOOT is not able to put them in right order. The mods gets unchecked when when you go to a new tab.
When I exit the game both gets unchecked. I now have to remember to check them before starting the game. So I assume this is the issue. I am having to rearange the mods according to LOOT with force enable game files disabled, then lock them in place to keep the order. But the mods always get unticked all the time.
Not sure why. Perhaps this may help.