I don't even know if this is the cause but I was just guessing maybe the game was getting confused with all the extra teams, but I do have the English league down to level 11 data added from FmScout.com. I have an online game with my brother and we're in our 3rd season and only 6 out of the 20 prem teams have been drawn into the FA Cup 3rd round. It's pretty strange. I didn't realise at the time but looking back at the FA Cup History in the 2nd season only 12 or so Prem teams got drawn into the 3rd round, but the 1st season was normal.
On further looking, 20 teams from League 1 or below should go into round 3 through qualifying from round 2. But there are about 35 teams from League 1 or below in round 3. Some teams like Charlton for example have been relegated and are in league 1, but automatically qualified for the 3rd round. Also Millwall for example have always been in League 1, but from season 2 onwards they have been automatically put in the 3rd round without having to go through the 1st and 2nd round. So the game is entering extra League 1 or below teams into the 3rd round automatically and some of the Prem teams are missing out all together. As I said i'm not 100% sure its anything to do with the added data but I've never had this problem before even though I had the lower league data on another save, and 6-7 seasons on everything is normal. Maybe other people have had the same problem and not even realised?
I've Just went on holiday to the next season to see if it would fix but it hasn't, only 5-6 Prem teams enter again. I also went forward again after removing every league apart from the prem and that didn't help either. So if anyone has any ideas it would be much appreciated. If not then we may have to start again. What English lower league databases does everyone else use?