There was a lineside fire which apparently was caused by electrical cables for the signal box. I was told by station staff at Sittingbourne that there was cable cut/nicked at the substation.
Whatever the real reason, there are no signals between Gillingham and Faversham, any train that goes to Faversham must be 'talked though' every signal. The only train to do this so far to my knowledge was the 1644 Cannon Street to Faversham, it took 2 and a half hours, most of the journey was from the Medway Towns to Faversham.
As for tomorrow, I was told to expect buses from Gillingham to Faversham and Sittingbourne to Sheerness, possibly a limited service to London Victoria, we'll find out more in the morning.
When I hear more, I'll try and post it as soon as I can.
EDIT:
http://www.kentonline.co.uk/times_guardian/news/2009/november/17/train_disruption_for_island_se.aspx
Found a link which explains what happened, I'll confirm it when I know.