Try this instead:
start-->control panel-->system-->advanced tab-->startup and recovery settings-->edit the system startup options-->this should open a notepad-->copy what you have there, and paste it here.
Copy and paste the current boot.ini file to a new notepad document, and save it to the desktop as bootOLD.ini.
Delete what is listed in the boot.ini file, and paste the following (assuming you're using XP pro.....if not, substitute your version):
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional" /noexecute=optin /fastdetect
That should make it ignore a false 2nd partition. Then you'll want to check the hard drive to make sure it's recognizing all of your storage space. If not, there is an existing partition that needs deleted.
If the first choice is D, then it should be your 'partition 2,' and 'partition 1' would be your C drive. Therefore, deleting the reference to the partition 2 in the boot.ini would remove that prompt on startup.
Right click on my computer-->manage-->disk management-->what is listed after each drive in the bottom window (ex: sysem, active, etc...).