Yea I figured out manually placing the esps from the zips, seems bad packing from their part. SMIM gives me some missing textures (smelter coal pile, some wooden stake formations mainly at watchtowers), which I find strange as it didn't do that with an older version of MO. Author of SMIM has noted that problem on nexus and just says, don't use MO : well, I can live without SMIM, but it was strange to run into that when I know it worked before.
So I'm trying to install some mods to my fresh Skyrim setup. The problematic mods appear on the left side list as intended, but nothing shows up on the right side. I've activated the said mods yes. The mods giving me grief atm are from the Populated Skyrim series( https://erkeilmods.altervista.org/skyrim/populated-cities-towns-villages-rs-relliosavini/), the Towns and Villages and one other which name escapes me, fails to give me an entry to the right side list. The other 4 ones work fine. I tested in game and confirmed that the 2 that do not give me the right side entries also do nothing ingame. Also, I tried to install Static Mesh Improvement Mod and it did not install correcly, I had missing textures ingame. The mod page does warn that the install doesn't work proper with Mod Organizer, but I had it working fine with an older version of MO. Any help on these issues is appreciated.