two references for you: 

http://technet.microsoft.com/en-us/sysinternals/bb963892.aspx

http://support.microsoft.com/kb/289022 

default=multi(0)disk(0)rdisk(0)partition(2)\WINDOWS says " the default choice is on physical drive 0, partition 2, in folder \WINDOWS"

multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Windows XP Media Center Edition" /noexecute=optin /fastdetect says "Windows XP Media Center Edition is on physical drive 0, partition 2, in folder \WINDOWS"

If you had installed a second OS, say Windows Vista Ultimate for instance, on the first partiton of the second drive (hypothecally) in your system, you might have an entry such as 

multi(0)disk(0)rdisk(1)partition(1)\WINDOWS="Windows Vista Ultimate" /noexecute=optin /fastdetect

To be honest, your post rambles a little, so I'm not sure exactly what it is you want to know besides how to understand what the boot.ini file is saying.  If you need more assistance other than the two MS references, just ask.

Charlie. 

Yes its normal, perhaps when you formatted you kept that D partition instead of formatting the whole drive.

if after your fresh install you deleted something out of D and something did not work right then the D partition is needed for  you run properly, in this case the only way to get ride of it is to format the whole drive and keep no partitions, create one new partition and install in that. 

     Hi Charlie,

          Thanks for the prompt reply I apoligize for the as you say rambling of my post !   What happens I want to provide more information then I probably need to not to mention the three cups of very strong java  ?   There you go a bunch of rambling  !   What  I basicially wanted to know is if my boot.ini file was what you would expect to see in a normal boot.ini , or if anything looked out of order ?  I hope this reply makes it more clear what I was asking for ?

                                     Thanks Again ,Gumba Nick

[boot loader]
timeout=3
default=multi(0)disk(0)rdisk(0)partition(2)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Windows XP Media Center Edition" /noexecute=optin /fastdetect

Most of the time, you don't need to edit boot.ini.  That's one of the reasons it is a system hidden file.  You probably know that.

If, for some reason (and I have done this), you wanted two versions of Windows XP on your machine, you might edit the description so you could tell the difference at boot time.

For the most part, you can maintain the contents of this file from the systems properties / Advanced / Startup and Recover page.  As Otiss indicates, you must have kept the installation on the D drive or partition, and deleted the installation on C.  It isn't important to Windows where it lives.

One thing to remember:  If you have more than one installation, regardless of version, you must install software on each version separately.  For instance, given two copies of XP, you might install MS Office in the version on C: in C:\Program Files\Microsoft Office.  If you need MS Office in the version on D:, you must start that version and install MS Office.  You can use the same directory if you want to.  All you're really doing is setting the registry for each Windows installation.

maybe i've had too much java.  time for a espresso home brew...