Alright, just as I thought it wasn't my fault and I did everything correctly. Now everything makes sense. The issue was wrong archiving option. I reinstalled my windows few days ago and downloaded the latest winrar version. When making an archive for MO to install, I always used basic "add to *folder name*" archive and it was working correctly, but with the latest version of winrar, after I made archive I would get "none of the available installer plugins were able to handle that archive" error when trying to install it with MO. I googled this error and turned out you need to use "add to" and then select archiving method as "zip" - this indeed allowed MO to install it, but as we can see, in game there were issues because of it. Either zip method does something wrong with the files while compressing them or idk. Anyways I didn't need to download older version, instead luckly there's also a "RAR4" compress option. I used it on my output and finally both MO could install it AND in game the files were also detected and working properly. That's why my old output made before formatting was working correctly, because it was made with older version of winrar.