PC taking a LONG time to load everything before the win logo, after BIOS update.

Every single time I turn on my PC, it takes a REALLY long time to start the first DOS-like screen and then it takes another while before the windows logo shows up. About 4-5 mins before the win logo. It used to be fast and sweet before updating my MSI MB BIOS...
It all started when I updated the BIOS the first time (I just thought it was something good to do). The start up took a long time like 25% of the times and it got worse every month. I tried changing the config in the BIOS but nothing helped, so recently I decided to update the BIOS again with a flash drive step by step as indicated in the MSI website with their software, only to find out that the problem got worse and that it happened 100% of the times I turn my PC on.
When the start-up is slow, it gets stuck in that black pre-DOS like screen, showing a "B4" in the bottom right corner. After that the usual first screen with some info shows up for about 3 seconds, then it all goes black again and shows some other pair of codes on the same corner (B2, A4,....)
Today I tried manuallly reseting the MB to see if it helped (I removed the battey for a while, then used the reset CMOS button to make sure). It did not help at all. I have tried changing the hard drives from IDE to AHCI but windows 8 won't start: after showing its logo for a while, it shows a blue screen of death with the sad smily :( and tries to reset (I have to manually reset it afterwards). I have one 2TB WD green hard drive and one SSD in which I have windows 8 installed.
I found some text today on the MB MSI website on the BIOS versions page... which I didn't see at the time, and it shows up only in my smartphone: "We recommend to only update to the M8 class module if you have an Ivy bridge processor. There is no way to go back to the previous M module after the update" (this is from memory by the way)
Something to add, I used the Crystal Disk Info software to check my drives and it showed the were in good condition. Then used CrystalDiskMark 3.0.3 to test them and got low numbers in my opinion; for the WD green
Sequential Read : 76 MB/s, Random Read 512KB : 26 MB/s, Random Write 512KB : 41 MB/s.
And for the SSD
Sequential Read : 167 MB/s, Random Read 512KB : 161 MB/s, Random Write 512KB : 111 MB/s
My relevant PC parts are:
Intel i5 2500k (sandy bridge)
MSI Z68A GD65 (B3)
SSD Mushkin Chronos 120GB SATA 6GB-s (windows 8.1 installed here) (MKNSSDCR120GB)
2TB Western Digital HD (WD20EARS)
2x Ati 6950 crossfire
I also already tried turning it ON with everything disconnected, changing the video card slots, using only one... etc.
Any ideas on how to fix this or what's causing it? I really need some help here... If you need more info, I will be checking this constantly and will deliver your requests.

Quote from: dan.djh on 30-November-14, 23:06:20
I already fixed the IDE to AHCI problem, which was the minor one. Solution for this: Use regedit to change HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\storahci\"Error Control" to 0 and delete StartOverride. Then you should be able to go into BIOS and change to AHCI mode. You'll need to do this again if you ever start up in IDE mode.
But I still need to fix the main one which is the slow startup... please help!
B4 is a USB problem! what USB devices do you have plugged in? (if its a keyboard and/or Mouse please say what they are like make and model!)

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Beelzebud wrote:
Ok today i noticed that if I delete ~/.nvidia-settings-rc, the UI loads instantly just like it's supposed to. I started googling around and found that there is indeed a bug in nvidia-settings which has something to do with the way it handles a machine's hostname.
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