Just to close this off.
It appears the problem was caused by our ISP timing out our ISDN dialup connection!
What would happen is that e-smith would dial up to receive mail, would start downloading it and then the connection would drop after 72 minutes (why 72 I don't know, but that seems to have been the limit imposed). Unfortunately not all of the email was downloaded in that time (we had over 100Mb waiting to be downloaded). The e-smith server would then distribute what it could then dial up again. Unfortunately the ISP had not marked the POP messages as having been downloaded, so then proceeded to download everything again. This is what caused the looping effect. My only guess to the disappearing e-mail is that the header was being downloaded, but because the rest of the message didn't complete the partial messages were discarded.
Can anyone tell me if this is an accurate guess, or just bunkum?
Thanks again
Richard