The 3.3 software with firmware version 36.10 was released in Jan 2013 and has some change that makes it work with Final Cut Pro X but breaks support for apps like Resolume and even FInal Cut Pro 7. This has something to do with CoreMedia vs Quicktime support if I understood the guy correctly. In the Sources tab you will not see the MXO2 listed at all. After reverting to 2.6.1 all available input settings return to the Sources tab and life resumes.
Fortunately you can update to the 3.3 software (with 36.10 firmware), uninstall it, then run the 2.6.1 software installer to add back the older support. This will remove support for FCP X playback.
Adobe Premiere, FCP X, and the latest AVID work with the newer 3.3 firmware. For FCP7, Resolume, and other general Quicktime support use 2.6.1.
Both software versions support the MXO2 Dock with Thunderbolt
