Just found this:

"The Rules Wizard rule reply using a specific template sends the automated
reply once to each sender during a session. This rule prevents Outlook from
sending repetitive replies to a sender from whom you receive multiple
messages. During a session, Outlook keeps track of the list of users to whom
it has responded. If you exit and restart Outlook, the list of which senders
have received automated replies is reset."

This sounds like it could be my problem. If so, what do I use instead? I
need to respond to every email - i.e. send multiple replies to the customer
because this acknowledges that we have recieved their order.