MSI C847MS-E33 + IBM serveraid M1015

Hi,
After many hours short on sleep this is the next stop to make.
I am building a homeserver and chosen this board MSI C847MS-E33 (flashed bios to latest version) for its celeron and low energy consumption.
At first i used a 430w psu(should have been just fine) and highpoint rocket sata controller.
Problem : disks controlled by the highpoint were dissapearing.
I replaced the psu as altho 430w should be enough (max load calculated +-400w) it looked like a psu problem.
Problem remained.
I checked out on the highpoint card and found more similar problems (driver problems under linux for the marvel chip)
So i replaced that one with the popular ibm serveraid m1015 wich is known to be a very descent card for its price.
The problem is now that the booting hangs on :
megasas: INIT adapter done
I'm using a debian based system.
I found a similar problem (other lsi card + mobo) here :
edit : links not allowed
He tried about anything i did.
There are a few things i have not tested yet :
(installing windows on that machine, altho running windows is not an option.)
I tried to boot with the latest ubuntu livecd and it failed aswel.
If i put this card in another computer everything works. (i will try to flash the cards bios tonight, it was impossible to do on the msi board as
1. I dont have a supported windows version (found out on other computer) that supports the software for updating.
2. It has been impossible to do on the msi board as linux wont boot with the card attached.
So i try tonight in the other computer with the ubuntu live cd wich does seem to boot fine with the card on that computer.
In the meanwhile :
Is there a known problem with this kind of cards (since i tried 2 cards and both gave problems) on this msi pci-e slot?
Any bios settings i should try?
Just anything else?
Regards.

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    Greetings,
    as advised by power member this topic was moved from discussion topic found here:
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    Built a new computer and decided to use the new LGA 1150 refreshed CPUs. Bought the MSI H81M-E33 Motherboard and installed windows. Noticed a problem with the rebooting even when installing windows. Thought it was just because of the windows installation, but problem persisted in which the computer seems to shut down but doesn't power down and i have to manually hold power button to power down and then push it again to start up. No real issues it seems since the computer does close processes and shut down but this was irritating me. I read online that BIOS updates seem to fix this problem. Did some research and decided to update with M-Flash to bios v6.6.
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    Decide to flash v6.5 in case 6.6 was too new and might some problems. However v6.5 has the same problems; bios update stops at 47%, computer attempts to reboot, can't reboot, I power off, power on, no signal, power off, power on, wait a while and it gets to BIOS (MSI Screen), then boots to windows.
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    TL:DR
    Had reboot problems decided to update BIOS
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    Update stopped at 47%, computer attempted to reboot, got no signal (reboot problem), powered off, powered on, waited a long time nothing, freaked out, powered off, powered on, waited a while got to bios (Whew), checked for new version (it is).
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    My questions are;
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    Was stopping at 47% normal?
    Should I try to update the BIOS another method to fix my current problems?
    Am I missing a step somewhere?
    Any help is appreciated, I just got really freaked out by the whole process but I'm just glad the computer still works (kinda).
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    -J
    Specs:
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    Intel i5-4590
    Corsair CX-430
    Crucial Ballistix Sport 8GB
    PNY Optima Series 240GB
    Seagate Barracuda 1TB
    LG 12x BD-Rom
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    MFlash reboots in the process. To be sure reupdate using the below instructions and archive for a proper fpt flash. If you used Win8 feature (fastboot) before the first update be aware taht you need to set anything again after an update (e.g. enabling safeboot) as everything is set to default.
    >>Use the MSI HQ Forum USB flasher<<
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         E.) Start the forum flash tool and select option 1. Then point the tool at the compressed archive we downloaded earlier. Then to your USB Flash Drive.
         F.) Boot to the USB 
         G.) Now follow the directions and let the tool flash
         H.) After flashing reinstall ME drivers in Windows:  http://download.msi.com/dvr_exe/intel_amt90_mb.zip

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