Check your boot order in the BIOS.
"Boots to the OS". Whatever your OS drives are attached to is booting first.
Make sure that the LSI is first in the HDD Boot order submenu.
Also, instead of 3 RAID controllers 1 RAID controller plus a PCIe Expander with 36 Ports might have been a better option.
Thanks for the response.
Currently there are no drives attached to the controllers or any other part of the server. I am still working on getting the PCIe cards to play nice before attaching (also waiting fro cable delivery ).
What I have discovered much to my surprise is that the cards will only be recognised in slots 6 and slot 3 (Slot 6 is the 16x mechanical / 8x electrical and slot 3 is the 8x mechanical / 4x electrical next to the PCI slot). Added to this is the fact that with both controllers in the slots mentioned above the board also does not recognise my Intel ET dual port network card in slot 4 (8x mechanical / 4x electrical). Looking at the technical specifications (v1, page 15) shows that slot 6 is controlled by the CPU (as are slots 5 & 4) but slot 3 is controlled directly by the C204 chipset. In the technical specifications (v2 post E3 v2 release, page 17) nothing appears to be different in the block diagram. Ihave also found that both versions of the tech specs list under section 3.4.2 (v1, page 22), and I quote...
Intel® Server Board S1200BTL
One PCI-E x16 connector to be used as a x8 link, two PCI-E x8 connectors to be used as a x4 link and one SAS module connector to be used as a x4 link connected to the PCI-E ports of the processor. One PCI-E x8 connector to be used as x4 link connected to the PC-E ports of PCH.
Now this indicates to me that slot 3 has a full x8 electrical link but slots 5 & 6 share a single x4 electrical link and slot 6 has its own x4 electrical link. Another x4 electrical link is reserved for the SAS module connection. Even so I would have expected that either slot 4 or 5 would have still worked. I have not tried the network card in slot 5 yet, I may do that when home tonight.
I also have an E3 v1 which I may also test out to see if that makes any difference. I have a horrible feeling that the revisions to the BTL prompting the BTLR may have been to get round this issue. I may have to fall back to the original idea of using the on-board sata and AXXRMS2LL040 sas add-on to get round this issue or use the RES2SV240 expander linked to the x8 card (slot 6) as well as the card in slot 3 if I can get the network card to work in either slot 4 or 5.
The reason for using multiple controllers rather than a single controller was mainly due to this server being configured as an VMWare vSphere host. One of the VMs, being a file server, is to have a controller passed to it via VT-d enabling the guest operating system to utilise NTFS on the disks. A second server is a backup server and will have at least 4 drives passed to it natively as well, again in order to enable the drives to be formatted as NTFS. The third controller was for the VM stores (VMFS3). The advantage for the drives being formatted as NTFS for the two VMs is that the drives can be unplugged and attached to any other Windows machine in order to get access to the data on them. This project has no budget for a second server as it is for a small family business with no real requirement for quick access to the data should there be a failure.