I am attempting to setup a htpc, with ubuntu booting from USB and 3 SATA disks as a raid array.

I installed Ubuntu 11.10 minimal to the USB device, everything was working OK for the first few hours, however after running apt-get upgrade, it no longer boots from GRUB2 (the usual blinking cursor issue)
However, it boots fine if I disconnect the sata HDD in the machine (so the USB device is the only boot device)

I am assuming (correct me if I am wrong) that the SATA disk is being assigned /dev/sda and attempting to boot from HDD, and therefore the USB device is getting the wrong /dev/sdX?

other notes, the sata disks are unpartitioned and pressing shift during boot does not bring up the grub menu also.

Thank you for your time