Ok...this took a lot longer than it should. But here it goes:

Installing 12.04 on a 64 bit system that supports UEFI booting like the thinkcentere will create three partitions on the system: a FAT partition for EFI, the ext4 partition for ubuntu and some swap. However, restarting the machine, I was not able to boot at all. Initially, the Intel Boot agent would kick in and try to boot from the network. Even if you turn that off, as indicated later, it still doesn't boot. It says no operating system found.

Now here are the things I tried that didn't work for me:

1. Change the SATA controller type to IDE Using a boot repair disk (it
   doesn't know how to handle EFI with GPT partitioning)


2. Changing the order of the boot sequence to put HDD first


3. Changing the boot mode from UEFI, to Legacy or to Auto


4. Recompiling GRUB2 and putting it in the UEFI paritition, as indicated here:https://help.ubuntu.com/community/UEFIBooting

The first good direction I got was from this thread:http://ubuntuforums.org/showthread.php?t=1896052 People were having problems with earlier versions of Ubuntu. One of the suggested solutions is to install 10.04 first, and update from there.

What this really does is forget UEFI altogether, and create just two partions..the ext4 for ubuntu 10.04 and swap. You could then upgrade to ubuntu, which keeps the same partitioning. A couple things to note...mind your architectures, since this particular machines support 64 bit or 32 bit, so the 10.04 you install first should have the architecture you intend to keep. Also, your network card will likely not work on the 10.04 kernel, so you will have to upgrade from the cd by installing the alternate iso. Follow these instructions: https://help.ubuntu.com/community/PreciseUpgrades#Upgrading_Using_the_Alternate_CD.2BAC8-DVD .

What I did instead was, First installed 10.04, then install ubuntu 12.04 again, but go to 'do something else' on the partitioning page...and i simply chose to reformat the main ubuntu parition and leave the swap as is (mind you, after 10.04 you probably have only those two partions on the HDD you installed the ubuntu on). [in retrospect, I could just have created those partions without installing 10.04, it seems]

Once installation is done, I restarted, but was greeted with an error "invalid arch independent ELF magic". Looking this up indicated that grub was probably from a previous version of ubuntu,and needs to be installed again. I had to boot from the liveCD/USB again, and reinstall grub2 (you can follow these steps:https://help.ubuntu.com/community/Grub2/Installing#Reinstall_from_the_LiveCD)

Alright, now restart again. It should boot, but I got some errors at the begining which said "no suitable mode found" and "no graphics mode found". Apparently, this is something simple that has to do with fonts. Found this bug report https://bugs.launchpad.net/ubuntu/+source/grub2/+bug/699802 and then used the workaround on comment #24 and viola. Now the system boots into 12.04 with no errors...it is using legacy booting...but it working for now at least.

I believe this can be fixed in the installation process of 12.04, but things are this way for now.