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Thanks for the info. If you are right, they will fix it by replacing the CPU Tray anyway. I may still let them do it this time, and keep the old tray as my own backup (of course, fix the northbridge as well).

The problem is that if they fix it by replacing the tray, it still can't 100% sure the problem is the northbridge, and I don't think that they can only test the bridge for me. (Of course, I will try to ask).

I did remove the CPU heat sink and check the northbridge, it looks normal. So, not the usual rivet problem. Of course, it can still be the northbridge. But I want to fix it ASAP, I don't want any more down time.
 
They don't have procedures, tools and knowledge for testing components of boards. It isn't that kind of service.
Find later a local workshop equipped with BGA soldering station, preferably with MacBooks fixing specialization and try.
 
Million thanks for the tips. Very useful, I now have a clear direction on how to do it.
 
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Problem solved, as we guessed, the CPU tray is faulty.

Apple charge $300 in total, for me, which is reasonable by considering they do all the tests, fix the problem by install the new parts, give me a simple system report (my old 4870 is faulty as well, but just the 3D part. I have a 7950 anyway), and extra 90 days warranty.
 
Problem solved, as we guessed, the CPU tray is faulty.

Apple charge $300 in total, for me, which is reasonable by considering they do all the tests, fix the problem by install the new parts, give me a simple system report (my old 4870 is faulty as well, but just the 3D part. I have a 7950 anyway), and extra 90 days warranty.

Problem solved, as we guessed, the CPU tray is faulty.

Apple charge $300 in total, for me, which is reasonable by considering they do all the tests, fix the problem by install the new parts, give me a simple system report (my old 4870 is faulty as well, but just the 3D part. I have a 7950 anyway), and extra 90 days warranty.

Great to know that your Mac Pro has been fixed and $300 is a good deal considering the type of repair that was performed. It's sometimes hard to find a reliable repair center. My cousin's Macbook Pro had boot up problems. He brought it to one Apple repair center and the technician said the logicboard needs to be replaced. Being out of AppleCare it will be a costly repair. He then brought his laptop to another repair center for a another check up. And the tech guy said it was only the hard drive that's busted. His laptop
 
I often wonder what type of training these Apple Store Techs. have. Every time I go to one of my local Apple stores, I only see pimply faced kids that could easily pass for high school aged. When talking to them about anything, it's clear that most of them only have enough knowledge to speak technobabble and impress people who know nothing about computer hardware. I dread the day when I actually need help with a difficult hardware problem.
 
Just realise an interesting fact. This repair fix my boot manager!

The combination of 5,1 firmware + the Sonnet Tempo SSD card suppose will break the boot manager, and it was.

I've try lots of reset and none of them able to bring this function back perfectly before my 4,1 broke.

Just now, my GPU has some problem. So I've try some resets and swap GPU to confirm that is the actual cause. During the process, I suddenly think that may be the boot manager is working, so I try. And amazingly it is working perfectly.

I am not sure if it's related to the repair or the multiple resets. Apple only install a new CPU tray for me, and that tray looks a little bit different than my original one. AFAIK, there are 2 versions of the 4,1 single CPU tray, and now I am having the V2 tray. May be this is somewhat related to the boot manager.

Anyway, I am happy with this result :D
 
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