The flex ribbon cable on my BD-ROM has gone bad and through unforuntate experience I realized something interesting. I don't know if it means anything but I'll say it anyway.
The GameOS operates without any issue at all without the BD-ROM Drive attached, however, using the latest otheros.bld, PS3 Linux will not operate as desired.
There is a extremely extended pause during the bootup sequence before the framebuffer appears, and when you do get to the kboot prompt, nothing exists on the hard disk drive.
Opening a shell in kboot then running fdisk shows a 10gb disk (I set my otheros to 10gb), however there are no partitions assigned. I created a partition then rebooted (since the device /dev/ps3da1 did not appear), and the same thing happened. When it came back the partition was gone.
Upon rigging my faulty cable enough for the drive to identify itself to the system (wont load or read discs, but will send its model data, ect), the kboot loaded at its normal speed, and my OtherOS data was untouched as if nothing ever happened.
So, in short, when the BD-ROM is not attached, the system shows a phantom hard drive. I wonder what this could mean, especially since, as I said, the GameOS has no problem running without the drive, it seems like it couldn't care less.