Just wanted to join the fray and see if my situation can help shed any light.
I'm a video editor, and I have a 2011 17" 2.2 GHz i7 MacBook Pro with 16 GB RAM which drives two Thunderbolt displays and a Matrox Mini MXO2 video breakout box, also connected via Thunderbolt so I can run an HDMI monitor for clients. Up until a month ago, I've been running FCP 7, After Effects, Avid, etc on my system with no problems; both screens looked and performed amazingly and my machine, although getting a little older now, worked flawlessly. The problem is, with new video projects having increasingly demanding specs (increased resolutions, higher bit rate compressions, etc) I noticed my eSata RAID enclosure was starting to bottleneck me. So I decided to look into upgrading myself to a Thunderbolt storage solution for hopes of taking advantage of the breakneck speeds, and also to future proof myself for a while. Instead of going for a Pegasus, I eventually decided to go with the Areca ARC-8050, an 8 bay Thunderbolt RAID enclosure that would allow me to bring my own hard drives to the party.
So I filled the thing with 3TB drives, set it up for RAID 6, leaving me with 18TB of useable space and set off to speed testing. I ran the Blackbagic Disk Speed Test and was not met with the amazing results I'd expected.
DUAL THUNDERBOLT DISPLAY TEST SETUP:
Total Thunderbolt Devices: 4
Chain order: MacBook Pro > TB Display 1 > TB Display 2 > ARC-8050 Enclosure > Matrox MX02 Mini
Results: 240 MBs Write & 300 MBs Read
While this was still a significant boost from my old eSata setup, I wasn't getting the near-SSD speeds I was seeing in benchmarks I had found online. So I scratched my head a bit, did some searching and stumbled upon an article claiming dual thunderbolt displays can cause a significant performance hit to a single Thunderbolt chain. GULP. Needless to say I was pretty disappointed with what I was reading, I'd just put a good $4,000 into building this Thunderbolt-heavy system, not counting my MacBook Pro itself. Here I am with only 4 devices on this Thunderbolt chain, which is spec'd out for 6, yet I'm maxing it out!? Here's the article in case you wanted to take a look: http://www.fcp.co/hardware-and-software/pro/715-does-thunderbolt-slow-down-when- daisy-chained-with-an-extra-display
So I went ahead and took one of my Thunderbolt displays out of the equation and tested the whole thing again. Sure enough my drive's performance nearly doubled! These were the kind of numbers I had expected.
SINGLE THUNDERBOLT DISPLAY TEST SETUP:
Total Thunderbolt Devices: 3
Chain order: MacBook Pro > TB Display 1 > ARC-8050 Enclosure > Matrox MX02 Mini
Results: 594 MBs Write & 467 MBs Read
What's most puzzling is that while the original dual display setup only yields 240 Read / 300 Write (which is still considerably faster than my old eSata drive could manage) real world performance in FCP and AVID is drastically worse than it had been with my eSata solution. I can't edit at all with both Thunderbolt displays in use, even with very low bitrate content - the footage just sputters chopily as if I'm taxing a 2006 machine with a 5200rpm drive. I've essentially bought and built a state of the art system that functions worse than any old one I've ever used!
So in closing, I'm not sure if this is a problem specific to you all with Pegasus drives, but instead a problem with the Thunderbolt technology / Apple's displays / or the way Apple is marketing Thunderbolt as an all-in-one solution for professionals. These Thunderbolt displays apparently suck up so much bandwidth to drive their 2560x1440 resolutions that my laptop's single bus can't even come close to supporting the 6 devices it's supposed to. At this point I've pretty much resigned to hoping that the new Mac Pro, with it's multiple busses of Thunderbolt 2 ports, will be my saving grace. While I wouldn't trust the claim that it can handle 36 devices via Thunderbolt, I'm hopefull it can handle the measely 4 I need!
I'm crossing my fingers that someone will come up with a firmware/software fix, but at this point I'm guessing I spent $4,000 onlly to learn that I need to drop another $4 or $5 grand when the Mac Pro comes out!