Right, just had a reply from Sky Sports.
Seems I got the captaincy change muddled...ie if you change your captain after the Saturday 12.45pm kick off it doesn't take effect until the next days matches, not the next scheduled matches

However if you log on right now the Transfer Deadline clock reads 00 days 00 hours 00 mins despite that we've still got around 50 mins to kick off. Sky sent me an email saying that as long as transfers are made before the actual kick off they will still be logged.
Code:
If you wish to make a transfer or captaincy change for today’s games then it needs to be registered before 12:45pm today, Saturday 2nd November. Any transfers or captaincy changes made from 12:46pm today will only become effective to score points in the games played on Sunday 3rd November.