Here's another data point. I had the exact problem described here when connecting an Apple 27" LED Cinema Display (the TD's predecessor) to both a retina MacBook Pro (mid-2012) and a mid-2015 MBP. Swapping out the MagSafe 1 to MagSafe 2 adapter did not solve the problem; if I used a newer Apple 85W adapter with MagSafe2 plug, there was a mostly reliable connection. Eventually, the intermittent charging problem seemed to get worse (sometimes I would have to "jiggle" the MS1-MS2 adapter several times to get the LED on the MS1 plug to turn on), and at wit's end, I took the display to a local Apple Store. The "genius" diagnosed a faulty video/power cable on the display itself, and offered to replace it for about $85. I agreed, and the new cable did fix the problem.
However, they also left streak marks on the LED panel inside the display, and after I brought the display back for them to clean it further, they concluded that they had damaged the panel and offered to replace the 27" LED Cinema Display with a Thunderbolt display. For completely different reasons, I also wound up getting a new MBP (mid-2015) a bit later.
Well, only a few months after I received a completely new display and a new MBP, the problem has returned! 😮 So I'm at a loss to explain this. I'll try swapping out the MS1-MS2 adapter, but I don't know how the one supplied with the Thunderbolt display could have gotten dirty or damaged in so short a time. It did work flawlessly for a while.