I have FINALLY discovered a work-around/solution for this situation.
(after spending 3 days, wrongly debugging the megaraid_sas driver source
code....)

Setting linux kernel boot parameter pci=conf1 allows my Intel RAID
Controller-RMS25PB080 (LSI 2208/Fusion based) to be detected, and the FW
to transition to Ready state.  Without this setting the Card FW responds
only with 0xF0000000 Fault (Masked).

I found linux kernel series 3.0.0 (as used in Oneiric / 11.10), properly
discovered and used the RAID card.  Things broke in kernel series 3.2.0
(as used in Precise / 12.04), onward.  So this also affects Quantal
(12.10), and current Raring 13.04 kernel builds (v3.7+).  So this means
in my Intel s2600 system, using the Intel/LSI card I have confirmed
broken PCI discovery in kernels 3.2 up to current day 3.7.1 kernels.

Details:
Card PCI ID: 1000:005b
Card PCI description: LSI Logic / Symbios Logic MegaRAID SAS 2208 [Thunderbolt] 
(rev 03) aka Fusion
Card Firmware Version: v23.9.0-0018 (most current to-date)
Card OEM: Intel RAID Module (Card) RMS25PB080 SAS
System Board: s2600CP - E5-2600 Xeon, LGA2011 Socket
System Firmware BIOS level: 01.06.0002 2012/11/15 (most current to-date)

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https://bugs.launchpad.net/bugs/1091263

Title:
  Cannot install Ubuntu Server on Intel Raid System

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