Update: It appears that the Snort version is the issue. Nitro only supports Barnyard2 v1.9 (with the nitro output patch), and it seems that newer versions of Snort write a differently formatted unified2 file format that Barnyard2 v1.9 doesn't parse correctly. A version I've gotten to work is Snort v22.214.171.124, however that is EOL by Cisco/Sourcefire and no longer receives rule updates. I've asked McAfee/Intel support what the most recent supported version of Snort is.
I only hope it's current enough to get rule updates.
If anyone knows of a more recent version of Snort that works with Nitro and Barnyard2, please post.
Did you get your answers and or find a working solution?
Intel has opened a task to update the Nitro patch for more current versions of Barnyard2, however there is no ETA. In the meantime, I'm using an old version (the oldest Snort permitted to continue to have a feed) and the deprecated version of Barnyard2. Snort version 126.96.36.199 still qualified for updates, and works with the patchable version of Barnyard2. Snort's EOL dates can be viewed here: Snort.Org