If it isn't hitting the queue at all and isn't going to the dead-letter queue, it suggests the item isn't being sent to the queue. You should be able to confirm that this is the case by switching on the journal for the queue.
Assuming it isn't hitting the queue, it is probably a transaction issue. I would check that you are definitely committing the message to the queue every time. Make sure there aren't any exceptions being thrown and swallowed that causes the transaction to roll back or never be committed (essentially the same thing). Also make sure there aren't any conditional statements that mean the commit gets skipped.
I would add some logging around every location where a transaction is started, committed and rolled back and also around any location where you are creating a message. You can then review you log to see the order of events and see what's going astray.
Another option would be to remove all of the transaction code and test the code against a non-transactional queue. If the messages all appear then it is a transactional problem. If not, the issue is elsewhere.
I use MSMQ a lot and the one thing I have learned through experience is that it works really well and the weak point is me :-)