Latest Update
First thanks to everyone for your continued input and ideas. This really is such a great site and forum full of wonderful and helpful people. I hope in the future I can help others out as much in return.
OK, so I had another email from Supermicro support today containing a private FTP link for me to use to get the fabled 2.0b version of the BIOS for the motherboard. They suggested that I flashed this first before doing anything else. So I did this, all went well no errors and I rebooted the system. Now all of a sudden I can't get into the BIOS. It just freezes with a _ cursor in the top left corner and a A9 in the bottom right corner. Hmmmmm
So I thought let's get back to basics. Powered off, removed all the cards, and powered on again. Started straight up and I got into the BIOS. All settings had restored to defaults so that might be why it wouldn't go in.
I put two of the cards in. Started with 5805 in slot 7 and the 6405 slot 5, where I want them to be in the end. Just as before runs the BIOS for the 5805 and the 6405 isn't even registered. Swapped over. Now the 6405 in slot 7 runs it BIOS first and just as before the 5805 crashes with corrupted firmware error of FF.
Back into the RAID card settings now to try what Adaptec suggested about disabling the Runtime BIOS setting in the 5805 card. Still the same issue with 5805 firmware crashing. Getting more confused and annoyed now
Suddenly remembered the PCIE Gen Settings. Changed this from Auto to Enabled as before and the GenX Setting to Gen2. Tried again and the same issues either way around.
So I enabled the Runtime BIOS setting in the 5805 again. Now I used the BIOS on the motherboard to disabled the OpROM for the slot that the 5805 is in. Start with 5805 back in slot 6 and the 6405 in slot 5...... Oh my Life.....
SUCCESS!!!!!
OK, now calm down again. Change the setting back and try it. Fails. Set it back again..... Success!
The Adaptec BIOS from the 6405 now starts. It finds the 5805 card then goes on and finds the 6405 card. All is good. This is how it used to work in my old Asus P5Q3 motherboard.
Now to put the other 5805 card into slot 7. This Supermicro BIOS is weird though it will only let you change the OpROM setting if there is a card in the slot. So second 5805 card in slot 7 runs it's own BIOS for now, sees the other 5805 card and ignores the 6405. As to be expected by past issues. Trouble is now when I try to enter the motherboard BIOS I get a big blue box saying "Saving Configuration Data. Press Enter to Continue". I press enter and everything freezes! And at 12:35am I need to switch it off and get some sleep.
I am now wondering if the 2.0b BIOS is having a few stability problems. The 2.0a version would let me in the BIOS every time with no issues. No matter what the RAID cards were doing. No matter what card I put in slot 7 it comes up with this blue box. I will try and get a picture tomorrow and post it here. It's not an exciting blue box like the TARDIS though
I may try going back to the 2.0a BIOS and changing the OpROM settings to see if that works. I had also downgraded the firmwares on the Adaptec cards after finding the mention about compatibility with the 6 series and 5 series in a 6 series BIOS update readme.
So small amount of progress made. At the moment I am concentrating on the RAID card issue. Will deal with the fan controller one when I have sussed this I think. Almost there, just pesky sleep and work keep getting in the way