Thanks both for your help, very useful. sys.databases showed as ACTIVE_TRANSACTION, so I ran DBCC OPENTRAN which showed this:
Oldest active transaction:
SPID (server process ID): 7s
UID (user ID) : -1
Name : tran_sp_MScreate_peer_tables
LSN : (549:456:1)
Start time : Jul 15 2011 2:12:01:687PM
SID : 0x01
E.g. since I last restarted SQL service. It is a bit odd as I ran dbcc opentran as part of my initial investigations and it did not show any open transactions. A bit of research then led me to this article about SP2 and log size with replicated dbs.
Which seems to be exactly the problem I am having, I will work through this when I am back in the office tmw and post results.