If the log reader agent is running, and changes are being picked up and sent out, and the sys.databases log_reuse_wait_desc for the publication database is showing "replication", then I'm not sure.

I haven't found a good source for replication internals so often take the shotgun approach, turning off transactional replication entirely and recreating the publications and subscriptions. That's an option for us anyway because we're just sending out data at night time. (Also we use replicate data only... so... it doesn't create and pre-populate the tables or anything costly like that).

So next choice: google log_reuse_wait_desc replication (like this hit: http://social.msdn.microsoft.com/Forums/sqlserver/en-US/633ea08c-942d-4703-bc03-f2befd35f612/log-file-size-keeps-growing-replication?forum=sqlreplication). And post back when you find out. Sorry I can't be of more help.