It sounds like your HDD(s) are ahead of the DVD drive in the boot order.
It probably worked the first time because the drives were completely blank, so it just skipped them and then booted from the optical drive. You tried to install, and a corrupted boot-loader (or something similar) ended up on the drives. Now they are 'sort of' bootable so you get that message and it never goes on to attempt to boot from the DVD again.
If there's nothing on the drives that you need to keep then go into your BIOS and ensure your DVD drive is in the boot order ahead of your hard drives.
Then boot off the Windows DVD and start again.
Also ensure there's not USB drives plugged in or floppy disks in the drive, etc. that it may be trying to boot off of.
I'm not sure why you were "messing around with the boot manager files" during your first attempt, as a basic Windows 2008 install on a fresh machine should be pretty much "OK, OK, Name, Key, OK OK, Finish" type of install, especially if it sees your hard drives first time without additional drivers. :)