Update: I upgraded to 64 bit Windows Server 2008 and things were running quite well. Then about two weeks in I installed the 7.0.?? flavor of BOINC and it wouldn't boot. I also applied a bunch of patches from Microsoft, so I can't say what caused it to fail. It couldn't find bootmgr. I had added a hard drive the day before to move the boinc folders off the SSD and also to put my media collection. Anyways, I re-installed windows server 2008 64 bit and all is well since.
I should know better than to go through a Patch Tuesday without a valid image saved on the NAS, but since it's an eval copy of ws2008 and I'm not putting my life on it I haven't. Besides, with the important things living on the second drive it's not so stressful when there's a failure to boot.
I was really trying to go Ubuntu on all my machines, but that's proved problematic enough that I have gone back to MS Windows on one of them, and will probably do the same with the other as soon as it burns through it's current set of WUs. As much distaste I have for Microsoft, at least their products tend to run well enough any user/admin intervention isn't needed very often at all. Perhaps I'll give Linux another try later, when the WS2008 eval license expires.
Ok the problem with bootmgr not found is that something or someone wrote an invalid set of start-up instructions to the boot sector and made it do that, second one of the updates could have done it and I recommend installing one at a time doing trial and error also it could be good if you had another hard disk installed if something goes wrong and requires an immediate system restore.
Even if you did save an image on the NAS it won't restore properly and since it is eval it won't let you do it, also a hard disk failure could happen at anytime and your data should always be backed-up somewhere on external hard disks, dvds, online storage, etc.
Ubuntu server is command line and you will need to be ready for the torture you will have with it, unless you know those command lines off by heart I suggest going to revise them even though I am a webmaster I still don't know all of them so its ok to admit it. If you don't like command line then go for the desktop instead of the server edition. Yes I also have hatred for Microsoft and they did ruin desktops by releasing Win8. Btw Ubuntu 12.04 is going to be released soon I estimate around another month of intensive beta testing then it'll be ready, already most of the people who use Ubuntu has already upgraded so if you do want to then by all means there's nothing stopping you. Here is the download section
http://www.ubuntu.com/download/desktop
http://www.ubuntu.com/download/server
I'll probably post more soon