I came know to about similar problem at one of client's setup. There fetchmail is running in daemon mode, with system wide config at /etc/fetchmailrc and no per user config.
# /etc/fetchmailrc for system-wide daemon mode
set daemon 600
set postmaster root
set no bouncemail
poll pop.ispdomain.com protocol POP3 user "firstname.lastname@example.org" there with password "secret" is user1 here keep nofetchall
There is similar problem, all mails are fetched every time. So, I came to understand that there may be some issues at ISP side, i.e. if ISP's servers are running some older version of softwares, then this might happen. The similar setup is running fine with other ISPs but just this ISP.