Hello toddalmond,
In reply to your PM about testing with a Virtual Machine and a faulty Master Boot Record.
I don't know about the Virtual Machine although my memory... (which is often faulty lol) tells me that there may be an issue there.
Turning to your real machine.
You really need an IT specialist who understands the 2003 Server but for what it's worth, here are some observations:
Problems with the Master Boot Record can be caused by a number of things including user error (i.e. user trys to do something that the system cannot execute or user changes something that should not be changed), corruption of one sort or another or a virus.
TechnicalIt is my understanding that Windows 2003 Server that there are technical issues that can cause difficulties in the MBR. This is not to say that your situation is a result of doing something wrong, rather just to alert you that things may not be as simple with that system.
CorruptionChkdsk may be a useful tool if the problem is caused by corruption although there are some things it can't fix.
To run chkdsk, open a command prompt and enter
CHKDSK /r /fIf your MBR fault is caused by general corruption or by infection, then, if you have the Recovery Console loaded (you have used/attempted to use ComboFix - it's possible CF has installed the RC), try booting to it and running the
FIXMBR command. This often works although some infections have a work around...worth a try though.
Logon to the
Recovery Console.
1. Restart your computer.
2. Before Windows loads, you will be prompted to choose which Operating System to start.

Use the up and down arrow key to select Microsoft Windows Recovery Console
4. You must enter which Windows installation to log onto. Type 1 and press 'Enter'.
5. At the C:\Windows prompt, type the following bolded entry, and press 'Enter':
fixmbrAfter that re-run ComboFix if you have been able to run it. Post the log back here.
MalwareToday there are a number of rootkit infections that infect the MBR. Some of the latest ones are very hard to detect. Depending on what sort of infection it is there are tools to deal with them on a standard machine but again I say some of ours may not work in your situation and in any case it is risky to use them on a machine they are not designed for.