It's probably because of default ports, no? Your SME will have its webpage on port 80 for http, and so will your FreeNAS. If I'm understanding you correctly, you probably have two things trying to be on port 80. Maybe you want to change the FreeNAS port to something else (say, 8080, is a common choice when there's a conflict), then you would access the SME on
http://128.1.2.3/ and you could access the FreeNAS on
http://128.1.2.3:8080/
(obviously replacing 128.1.2.3 with the actual IP, duh).
The option for the FreeNAS port is right in the GUI/system setup.
That's, *IF* I have inferred what you're saying correctly. You didn't give a lot of details on how you were set up.