Call LSI if needed for advice. They have awesome phone support. VMware has no support for small businesses.
First you should update the firmware on the LSI card. I cannot remember exactly, how but it involves making a dos -bootable usb drive.
But you must be able to see the LSI card bios come up on boot. The card works best in the top most (most inner) slot. Fiddle with the pcie settings in bios. There is also an excellent thread on hardware forums. Lots of info. My details from a long time ago are in there:
http://hardforum.com/showthread.php?t=1666761
Old: http://hardforum.com/showthread.php?p=1038350129&highlight=#post1038350129
Update with LSI firmware upgrade: http://hardforum.com/showthread.php?p=1039443025&highlight=#post1039443025
I have built another similar machine since and it went much better after upgrading LSI card firmware.
Good luck!