Binary package hint: debian-installer
Test system: HP DL385 G2 with a SAS controller in slot 1 and a FC controller in slot 5 (slot numbers according to the BIOS POST). Jaunty daily alternate CD downloaded last night (2009-01-14)
The SAS controller has disks, the FC controller does not.
The installer runs fine up until the disk detection part. It appears that the two CCISS controllers have come up with the FC controller listed first (c0d0), but obviously since it lacks disks it is useless. Partman complains about being unable to read the geometry of the disk and presents Ignore/Cancel options. Neither is a useful route in this case - what would be better would be an option to move on to the next available disk (c1d0) and try that.
There should be no post-installation issues that I can think of - the BIOS will not try to boot from an empty card and then everything from GRUB upwards should be only caring about the UUIDs of the filesystems.
(indeed, a preseeded hardy installation does indeed boot correctly)
Just to add a little more detail:
* Choosing either Ignore/Cancel leads straight back to the full menu of installer steps
* (almost certainly irrelevant) it's not a FC controller, just external SAS
* replacing the card after installation does not affect booting the OS, it comes up fine (as one would expect)