I returned my first mini in early November because the Thunderbolt port died and the HDMI port was flaky. After hearing that the blinking issue was fixed with the firmware update, I ordered another mini. It arrived yesterday afternoon and, in less than 24 hours, the Tb port died again. The first mini's Tb port lasted about a week or so.
Tried the usual troubleshooting dance of reseating the Tb->DVI cable, swapping monitors, log in as another user, reset SMC & PRAM, boot in safe mode. Still dead.
Called AppleCare and was escalated to a senior tech. He was great but had no other suggestions. He suspects it could be a bad adapter cable. Why the cable would work on the first mini and then die permanently, work on the second mini and then die permanently seems unlikely to be the cable, but I agree that the mini needs to be tested with a new adapter so …
… the phone rep called a local authorized repair center and they didn't have the ability to verify the adapter. Wow! So much for being Apple authorized.
My only choice is to go to the Apple Store in a mall that's under major construction so parking is horrible. And it's the last weekend before Christmas. Ain't gonna happen. Besides, this is the same store where a genius turned me away the first time without even looking at the mini or the adapter saying he'd seen it before and it was a common problem. If he would have tested the mini with a new adapter and tested the adapter with another computer and monitor, I wouldn't be facing another 40 km round-trip and an hour of my time.
My bet is that the Tb port has indeed died. Am I unlucky to get two minis with the same problem? Is this endemic to the mini? If so, I would have expected another report on this thread. Is my monitor somehow damaging the port even though it's buffered by the adapter? It's the same monitor I've used for 4.5 years on my 2008 MacBook and on several other computers.
On the bright side, I haven't seen any HDMI flickering so far although I've only used it about 6 hours.
I'll get the mini and adapter tested at the Apple Store between Christmas and New Years. If the mini is declared dead I'll have to decide whether to use the three strikes rule and give a third mini a chance, or to see if I can cough up the money for an iMac, which I really don't want.