Its weird because its fixed itself now. It happened after I tried an online co-op game (incidentally this was the 1st UEF mission - and when I won it said "Operation Completed" but clicking on the message didn't do anything and I had to kill Forged Alliance to exit). Since then I went online, started a skirmish and exited. When I go offline and start forged alliance from my offline shortcut it now connects to the lobby with no problems.
Thanks for the swift replies anyway. I am taking a week off from FAF now so my eyes can recover from the appalling lobby colours