I have a nexus and an S3 and it works fine. I tried replicating the issue and it worked fine for me. First question is, are you on a custom ROM? Not sure if that has anything to do with it, but just putting that out there.
Second, my nfc settings on S3 are with android beam on, so beam off.
Also make sure that you are placing the nfc sensors together, as it can be difficult to find on the nexus.
Lastly, I love using an app called SuperBeam, which allows me to share files between my two devices. It's like S beam for galaxy phones, except for all nfc android phones.
Best of luck!
Sent from my Nexus 7 using Tapatalk HD
Phone: Samsung Galaxy S3 I747M
Tablet: Nexus 7 (2013)