I have checked many times, my mod, the World Cup European area qualifier does not have the issue, 10 groups first plus 4 additional match winners ,total 14 teams enter the world cup.I also taught the national team of Gibraltar and won the first place in the qualifying group and successfully entered the world cup.The worst possible bug just happened. I fought hard to win our qualifying group as Gibraltar. But when the world cup came around, we were not in it somehow. I saw other of your custom teams in so I know they can be. Teams that didn't win the qualifying I played were in and some that didn't were; it was like it just completely ignored the qualifying results. Please look at this. If you can't count on being in competitions you qualify for, this excellent patch doesn't mean anything anymore.
I'm downloading your other patch that only works in tournament mode to replicate the experience I should have had in career.