Vista Installation Problems

Hope this is the right place for this, I recently re-installed 64-bit Vista on my new 10k Hard drive and I've run into some very unique problems.

I did the installation and it looked like nothing went wrong, it then rebooted as usual and then I got the "BOOTMGR is missing" when booting up. At this point I restarted and booted into the CD again, to manually re-install the BOOTMGR through command prompt. However when I booted into the CD it said I didn't have access when I tried to re-install it, so I booted into windows for the first time (using the CD I can bypass the BOOTMGR issue).

Curious as to why I couldn't get access the CWindows directory I took a look into it and found that I couldn't do -anything- to the folder/sub-folders. If I changed the permissions to give me as the user full control and ownership to the folders, I would get a "cannot access" error, making it impossible to re-install the BOOTMGR (also I'm rather dubious about even keeping the install as it is without control over the Windows directory).

Now is there anyone who has come across this before? as I am baffled by it and it's the second time I have tried to install it onto this hard-drive, without any luck.

Specs:
P5N32-SLI
Q6600
1x 80GB 10K Raptor Hard drive (Drive I'm trying to install too)
2x 250GB HDD (One with old Vista install, other with a temp XP install)
1GB RAM (Only been using 1GB during the installation due to prevent the BSOD)
2x 512MB 8800GTS
750w PSU

Any hope will be appreciated, thank you for reading.

It appears I may of found a solution, chatting with a work-mate it might be due to the old Vista installation, maybe I should of been concentrating last night rather then playing Guilty Gear X-2.

I'll report back what the results, someone else might have a similar problem.

Thanks for the link scotteq. Now I have system repair boot disks for my four Vista machines. I thought something was 'missing' when I ttied to do a boot to OS disk repair on one of Vista 64 installations. So, the retail version has the boot to disk repair console? OEM has only fix boot repair function? Anyway, thanks again for the link and great information. Maybe I won't have to reinstall the OS next time. 8)

I have OEM disks. When I boot to them, I can do a 'boot manager' repair sor of thing, but not a repair installation like XP.

Right I removed the extra hard drives, leaving just the intended OS drive. Installed perfectly, no problems as of yet. Thanks for your replies, it looks like the old hard drive with Vista on it was interfering with it.