(Before anyone mentions it, I've read
this thread 
)
I'd created all the missing players for my local non-league club, and transferred in those players who have recently signed. But every time I started a new game, only 8-10 of the 25 players were showing up, with the rest of the squad made up by computer generated youth team players.
The problem was that I was using an .edt file to swap my favoured team with another. As soon as I made the change with the editor (and then removed the .edt file!), all members of the squad were displaying.
I hope this helps some-one.