Dirk:
I cannot completely address the anomalies of AV & IPS. We tried implementing them but found with our large site (20K computers) that the fortigates just couldn' t handle it. Being an educational institution to boot, the students tend to kick the tires much more then corporate or institutional clients.
However, even with an av/ips free active profile list, the av & ips engines are running. They are what inspects the packets cached by the proxy service (thttp) and enforce the policies you have in place. You might want to check " diag sys top 1" and see how those services are running. If they are pegged the issue may be there.
I have done some dos based ftp but not through the the fortigates. Just as a test, I used ftp to get putty from simon' s site & my files matched.
I would suggest, if you have a support contract, that you open a call ticket.
Victor
P.S.: If you do implement AV, take the default file size of 10 and reduce it to 4 or lower on any of the protocols that you' ve activated. How many viruses/worms/trojans do you know that have sizes in the mb range?