I am no expert, however, I also had a simular problem
where one of two computers was causing e-mail to disappear
from the other. This user had two computers setup using
the same e-mail. One computer using Outlook 2002 was setup
at a remote site using POP3 to recieve her e-mail. The
other computer also Outlook 2002 was setup at the main
office using an Exchange server. On the computer using
POP3, the settings in the advance options would not keep.
I would check the box asking to leave a copy of the
message on the server. However, when I closed Outlook, the
setting would not stay. I installed all Window OFFICE
UPDATES and the Advance Setting worked and both computers
recieved e-mail without dissapearing. Best of luck.