I cam across these steps to solve your problem.  I hope this works.

If you have every spent any time supporting Windows boxes this error will be very familuar to you. Every once in while when you reboot a workstation or server you'll get the famous NTOSKRNL.exe is Missing or Corrupt error  Windows NT could not start because the following file is missing or corrupt:
         C:\Windows\System32\Ntoskrnl.exe
It's fairly straight forward to resolve this problem. Start by booting your machine from the install media when prompted follow these steps
- Boot to the recovery console (http://support.microsoft.com/kb/326215)
- Select your Windows installation that you want to recover
- When prompted provide the local administrator password
- Once you are into the recovery console you will probably be sitting at a C:\WINDOWS prompt
- Change the directory to the i386 folder on your CD / DVD drive (If you only have one partition it will most likely be D:\)
- Copy the following files to the C:\ drive
        copy ntldr C:
        copy ntdetect.com C:
- Change your source directory back to C:\Windows
- Next you will need to fix your boot record
       fixboot C:
- Most likely you will also have to fix the boot .ini using the bootcfg command
 bootcfg /rebuild
- Add the required Windows installation to your boot list
- Add the Load Identifier (Custom description)
- Add the OS Load Options (/fastdetect)
- Type exit to reboot the machine
Your machine should now be recovered from the NTOSKRNL.exe is Missing or Corrupt" error. If you are looking for a little more detail here is a pretty good post. Use this information at your own risk

http://the-it-trenches.blogspot.com/2011/03/windows-boot-error-ntoskrnlexe-is.html

I think I came across a similar post, I think it relates to Windows 2003 Srv

Can you copy the ntoskrnl.exe from the CD/DVD to C:\Windows\system32\ntoskrnl.exe ?


Do following command with the CD/DVD
(assuming it's mult-processor)

For Multi-Processor systems:
expand <cd-drive>:\i386\ntkrnlmp.ex_ <hd-drive>:\Windows\system32\ntoskrnl.exe


http://support.microsoft.com/kb/314477

Those instructions won't work for 2008.

I would run a check on the hard drive (chkdsk /r) and RAM.  Time consuming I know, but either could cause your issue.  You might also try rebuilding the BCD.

What is running on the server (what roles does it have)?

I'm not exactly sure what went has happened but Ive come in this morning after leaving the box powered down and it booted straight into Windows?

I'll leave the post open for a few days to see what happens.

Well, that's good news.  It does push me to think that it is hardware related though, as they tend to exhibit more of these transient errors.  For example:  a sector on a hard drive might be able to read once but not another time; RAM might test good in one pass but show errors in subsequent passes.  Allowing the machine to sit unpowered would have just allowed heat to dissipate which could be a factor.  If you've got the time I would still run the checks I proposed.

I will do, but will probably wait until the weekend, where I have more time to put it right again.

The machine myseriously managed to sort itself out??