you cant boot from the scsi drive if you have a pci scsi controller. same with any other hard drive controller. say...you go buy a PCI pata raid card. then you connect the hard drives to the card. you wouldnt be able to see the drives from the bios. same with this drive. you need to load the drivers from OS level, so that the OS can see the drives.
That is not true, actually. You certainly can boot from a PCI card ... whether RAID, SCSI, or other.
When your PC boots, it first runs through the motherboard's BIOS ... and you're right, at this point, it won't 'see' the drives attached to the card; it will only see the card itself.
The next step, however, is to launch the CARD's bios, which happily detects and configures the drives attached to the card. After this step, it will proceed to launch the OS.
I can see two possible problems.
There might be a problem with your boot loader's configuration. If the boot loader is not looking for a scsi card, or if it is not configuring it properly, it won't be able to boot from that drive. If you cut and paste your boot loader's config file, we might be able to find the problem (assuming it exists).
The second possible problem is that your SCSI driver's may be loaded into the kernel as a module, rather than built directly into the kernel itself. Modules are located on /root ... and if /root is on the SCSI drive ... well, you have a problem! In other words ... the SCSI module won't be inserted into the kernel until after the kernel looks for the boot drive ... which it can't do because it doesn't have the SCSI module loaded. So .. make sure that your drivers are compiled directly into the kernel and NOT being inserted as modules.
Hope this helps.