I am having the exact same problem. As you noticed in your experience, Peter, phpList 'appears' to be sending a much higher number of messages out than there are subscibers in the list. However, I don't think it is just a matter of 'appearing' like that. I think phpList is actually sending more messages than just one to each subsciber.
The reason I think this is that in the last two days my hosting provider has repeatedly blocked my account and reset my email password because their anti-spam server scripts have picked me up for sending out messages at a higher rate than the server maximums.
I have been in active discussion with the hosting provider helpdesk over this and have tried to throttle phpList appropriately to send emails out well within the maximum limits.
As per the recommendations of my hosting provider, I now have the phpList config set to batch sizes of 75, period of 1800 seconds and autothrottle set to 'on'. As I watch the list being processed, it 'seems' to only send 3 messages every 72 seconds (a rate that reflects my config settings) but then it stops sending...seems to freeze. I think it is stopping because the server scripts of the hosting company are automatically resetting my password when my message volume exceeds their limits. This is causing phpList to get stuck and seems to send it into a loop. The only way I can get it out of the loop is by going into the database and changing the message status from 'inprocess' to 'suspended'.
I should say that my mailing lists are very small (360 subscribers on the list I have been trying to process today) and I have been using phpList for years successfully without this kind of issue.
I am running version 3.2.6
Like Peter, I really need help with this issue,