I'm having this same issue on a brand new TBD and rMBP 15" (like bought within the last week).
Randomly I will see the TBD go black, then it will come back and I'll have the display, but my USB ports will stop working. I originally thought it was an issue caused with an Aune T1 USB DAC/Amp I was using, so I disconnected it. Then I thought it might be Steermouse for my G400s, so I uninstalled it and rebooted. Unfortunately that doesn't appear to have resolved the issue. It's very intermittent, but nonetheless is happening.
My hardware details are below:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro11,2
Processor Name: Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
Boot ROM Version: MBP112.0138.B07
SMC Version (system): 2.18f10
System Version: OS X 10.9.5 (13F34)
Kernel Version: Darwin 13.4.0
Boot Volume: Macintosh HD
Boot Mode: Normal
Thunderbolt Display:
Vendor Name: Apple Inc.
Device Name: Thunderbolt Display
Vendor ID: 0x1
Device ID: 0x8002
Device Revision: 0x1
UID: 0x0001000000000000
Route String: 1
Firmware Version: 26.2
Port (Upstream):
Status: Device connected
Link Status: 0x2
Port Micro Firmware Version: 2.0.7
Cable Firmware Version: 0.1.18
Cable Serial Number: C4M431400MFDNWFAZ
Port:
Status: No device connected
Link Status: 0x7
Port Micro Firmware Version: 2.0.7
From what I've seen in this ~30 page thread is that it appears most people have attributed the issue to a faulty All-in-One TB cable off the TBD and that replacing this with an external 3rd-party (OWC or other) TB cable fixes the issue. I'm going to try that to see if it resolves the problem, but as an interesting point on this almost every one of my coworkers with a similar configuration has the same exact issue, except for those using older (non-Retina) MBPs which seem to have no problem with their TBDs.
I'm pretty surprised that this issue has persisted more than 3 years considering the cost of a MBP + TBD is >$3000. It's beyond ridiculous this has not been resolved at this point.