Issue with repository and mods

Recently I have had some issues with mods folder and repository.

1) I have to activate mods each time I start the game for them to show up in-game (shortcut says all are activated, but they are not. When I activate them, the thumbnails load in and it is fine until the next time I start BeamNG)

2) I can't download new mods (in-game repository doesn't start downloading the mods, only the circle is spinning. Downloading from online to mods folder manually doesn't work also as mods don't show up in-game)

3) I deleted game via steam and deleted the Documents folder, but this didn't fix the issue. Mods from repository could be downloaded, but once I put in my 50 non-repository mods in the mods folder, they don't show up and in-game repository doesn't work.

Note: I had these issues prior to 0.14 update, but then I somehow managed to fix somehow by deleting the whole game and putting mods back in

Please send help

 

Thanks, you were a bunch of help, my issue is now solved!
I slowly dropped the mods back in and found the issue to be a duplicated map, which was both in repository and maps folder - Crash Hard Track
Turns out I had some more of such duplicated mods, but for other mods the game just throws out a warning message saying there is a duplicated mod. Not for this one though. No idea why it broke my mods, but everything is fixed now.