I have a 6-core 2013 MacPro and an Areca 8050 (original Thunderbolt 1) enclosure that have been working fine since January. However, since updating to 10.9.4 and iTunes 11.3, I have been getting a kernel panic on startup. The only way I could boot successfully was to disconnect the 8050, then reconnect it after logging in. After that, everything functioned correctly, but the 8050 had to be disconnected in order to boot.
I just spent two hours chatting with Apple support, and they helped me trace the issue to the iTunesHelper application that runs under the Login Items for each user. Once I removed this application from Login items, the MacPro booted successfully with the 8050 connected, and it has been working fine since. The support tech I worked with said they would escalate this issue to the development team for review. I also wanted to get the word out here in case anyone else encounters this issue. I hope this saves someone from spending hours trying to work through this issue.
2013 MacPro 6 core 3.5 gHz, 16GB RAM, 1TB SSD, 2012 rMacBook Pro, Areca ARC-8050, Final Cut Studio 3, Final Cut X, Adobe Production Premium CS6, Logic X