Mac Pro 2006, no display, TDM works. Video uploaded. Been to Apple.

Hi,
I have a Mac Pro 2006 and it's ben broken for a little while now. I tried all I could to fix it, reset everything, pressed all reset buttons on Logic Board, changed GPU. But the problem remains. When I start it the mac chimes, as usual and starts up in Target Disk Mode if I hold T (as it's obviously supposed to). The video shows you what happens when I start it up in regards to diagnostic LEDs.
http://youtu.be/jCMPG7Be9WE
Back in the Autumn I took it to an Apple Store. They said it needs a new Logic Board. I don't believe they are correct. If it starts in TDM and starts in alternative boot mode (holding alt key) but does not display anything surely it is a different issue and I shouldn't have to pay for a new LB, which they quoted me £300 ($500US) for?
Can anyone offer any suggestions?
Thank you.

My MacPro 3.1 (QuadCore 2.8 GHZ, 8 GB RAM, ATI X2600, Mac OS X 10.6.1) has the same Problems for some days.
At first I thought it didn't boot up at all, just after several trials....
Then the screen kept blank for several days....
Today I realized that it was booting and kept running until sleeptime.
Via remotelogin I can see a smaller desktop, Aperture tells (my iPhone has new Photos and Aperture is my default for iPhone synching) me the GPU is not supported and SystemProfiler reports that the GPU is not recognized.
I don't know what's happening, I had some graphical faults in the past week (the space for the fast-user-switching-name was blank for a few days and so on, reboots helped)...
Then the disks (booting Leopard from a 2x500GB RAID-0) were just recognized after every 4th to 5th reboot...
Seems to be really a GPU Problem, will try to swap the ATI X 2600 from one slot to another within the next days...

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