Hello,
I have exactly the same problem as you.
The problem is the two folders that are necessarily installed in the mod directory (millenaire and millenaire-custom), technic launcher don't like them.
In my case, i've also a ressource directory from ruins mod, and it's exactly the same problem.
If you find a solution, I'm interested.
And if I find it, I'll help too.
PS: Sorry for my English, I do for my best