Okay, as far as I see it, you are on a periodic tenancy now since your initial period expired 25/06/14.
In the absence of any clause in your contract to the contrary you would normally give one month's notice usually before the payment date ( which would have been 25th) so they are probably within their rights to argue for September's rent. In no-one's world will they swing a fixed term tenancy until January.
Now regarding your deposit, they sound savvy so you won't be getting that back in a hurry as nearly all agents try to find a pretext to keep it, however if they have not protected it then they may be liable to pay you up to 3 times the deposit amount so send them a recorded delivery letter formally requesting details of the deposit and under what scheme it is held. If they do not or cannot provide this you hold the advantage.
Keep us up to date with what they say regarding the deposit but you should be able to find out yourself by entering your details in the tenancy deposit protection websites.
You can find those here:-
http://www.depositprotection.com/
http://www.mydeposits.co.uk/
http://www.tds.gb.com/