mysqldump not exporting all tables
When you have a database with that many tables, what must you remember ???


Use --single-transaction with --no-create-info : This will produce a dump of all table data with the same point-in-time
Setup Replication : You can run STOP SLAVE; and then run your mysqldump, assured that no other activity in going on in the Slave. When dump is finished, that run START SLAVE;.
Don't do any DDL during the dump : Running DDL while dumping from a MySQL Instance can produce some spurious actions (dump reload not completing, wrong structure of table prior to data reload, and things like these)


If your database is all-MyISAM (you start hearing Twilight Zone music) : Don't mysqldump. Shutdown mysql and maker a copy of /var/lib/mysql (LVM Snapshot, scp, rsync, etc). That way, there is no SQL controversy.

You should probably dump data and table structure together, just to be sure.