Every so often I run into a problem and its solution that reminds me that computers are weird.
I bought a Dell PowerEdge 1800 server with a very nice RAID card but no hard drives for $50. I was a deal - two dual core 3 GHz Xeon processors and 4 GB of DDR2 ECC RAM were included. I tested the RAM with memtest 86+ for over 18 test cycles and it reported no errors - so I stuck an Ubuntu 12.04 CD in the CD drive, booted off of the CD, and started the installation - which seemed to complete properly.
I wondered if it was looking to boot from the RAID card? Nope, that's not it. Are the boot order and boot devices properly specified in the BIOS? Yes they were.
I finally went through all of the hardware BIOSes on it - there are three or four. I saw the PXE boot (from the network) configuration display was set for 2 seconds before it turned off and you couldn't get into its configuration. I thought that value was a bit quick and changed it to 5 secs. - lo and behold it booted from the hard drive!!!!!
I speculate that one of two things happened - either it was set to PXE boot and that was still stuck in its head (the reason for a PXE boot in a file server is so that you have one more slot in the case for a disk).
Or that it wasn't getting enough time to check the boot order.
I'm now happily updating Ubuntu 12.04 in preparation to install Amahi on it and use it as a file, media, and VPN server.
The moral of the story? Try changing something even when you don't think the change is related to your problem - it might fix it, because computers are weird.