If you are scanning on the outside of a perimeter device, then what
would be useful would be a "diff" of a scan results from the outside
scan and the inside scan.

Several other comments:

- if you are comparing the results of a manual inspection of a Windows
server with a remote firewalled Nessus scan, you are sort of comparing
apples and oranges. If Nessus can't reach port 445 or you are not
scanning with credentials, you will find less "missing patch"
vulnerabilities.

- the application proxy *may* be dropping packets because of a filtering
rule that completely blocks access to a certain port or IP address.
However, I question how much of an application proxy would filter a
probe from Nessus. Some firewalls recognize "scanning" and will drop the
connection. Some Nessus checks may break a protocol like HTTP, but I
would be very surprised if this was so and an application proxy dropped
the connection. To really see the impact of the proxy or firewall, I'd
look at it's "deny" logs.

- there may be other limitations in the firewall like maximum number of
connections and such.

- although mostly NAT focused (you didn't mention NAT or port
forwarding, but it may be relevant), I've blogged about scanning hosts
from inside and outside of a firewall with Nessus previously:

http://blog.tenablesecurity.com/2006/08/using_nessus_to.html

Ron Gula, CTO
Tenable Network Security
http://www.tenablesecurity.com




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