http://support.microsoft.com/kb/927392 may solve your issues, I had a problem where putting in XP/Vista32/Vista64 I screwed up my bootloader and I basically (following those instructions on a x64 system) went in with any disk that can let you get to the command prompt (x86 or x64 and build of vista) and deleted the entire bootloader directory then recreated it, booted into Vista then just fine and used EasyBCD to add in my XP and Linix boot drives and away I went happy as a clam.
P.s.
I also suggest getting the iReboot utility, it's quite nice and handy.
Addendum:
You know what I just figured I'd post it in here, save yah the hassel =P
INTRODUCTION
You can use the Bootrec.exe tool in the Windows Recovery Environment (Windows RE) to troubleshoot and repair the following items in Windows Vista:
•A master boot record (MBR)
•A boot sector
•A Boot Configuration Data (BCD) store
Note When you are troubleshooting startup issues by using the Windows RE, you should first try the
Startup Repair option in the
System Recovery Options dialog box. If the
Startup Repair option does not resolve the issue, or if you must troubleshoot more steps manually, use the Bootrec.exe tool.
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MORE INFORMATION
To run the Bootrec.exe tool, you must start Windows RE. To do this, follow these steps:
1.Put the Windows Vista installation disc in the disc drive, and then start the computer.
2.Press a key when you are prompted.
3.Select a language, a time, a currency, a keyboard or an input method, and then click
Next.
4.Click
Repair your computer.
5.Click the operating system that you want to repair, and then click
Next.
6.In the
System Recovery Options dialog box, click
Command Prompt.
7.Type Bootrec.exe, and then press ENTER.
Note To start the computer from the Windows Vista DVD, the computer must be configured to start from the DVD drive. For more information about how to configure the computer to start from the DVD drive, see the documentation that is included with the computer or contact the computer manufacturer.
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Bootrec.exe options
The Bootrec.exe tool supports the following options. Use the option that is appropriate for your situation.
Note If rebuilding the BCD does not resolve the startup issue, you can export and delete the BCD, and then run this option again. By doing this, you make sure that the BCD is completely rebuilt. To do this, type the following commands at the Windows RE command prompt:
•bcdedit /export C:\BCD_Backup
•c:
•cd boot
•attrib bcd -s -h -r
•ren c:\boot\bcd bcd.old
•bootrec /RebuildBcd
/FixMbr
The
/FixMbr option writes a Windows Vista-compatible MBR to the system partition. This option does not overwrite the existing partition table. Use this option when you must resolve MBR corruption issues, or when you have to remove non-standard code from the MBR.
/FixBoot
The
/FixBoot option writes a new boot sector to the system partition by using a boot sector that is compatible with Windows Vista. Use this option if one of the following conditions is true:
•The boot sector has been replaced with a non-standard Windows Vista boot sector.
•The boot sector is damaged.
•An earlier Windows operating system has been installed after Windows Vista was installed. In this scenario, the computer starts by using Windows NT Loader (NTLDR) instead of Windows Boot Manager (Bootmgr.exe).
/ScanOs
The
/ScanOs option scans all disks for installations that are compatible with Windows Vista. Additionally, this option displays the entries that are currently not in the BCD store. Use this option when there are Windows Vista installations that the Boot Manager menu does not list.
/RebuildBcd
The
/RebuildBcd option scans all disks for installations that are compatible with Windows Vista. Additionally, this option lets you select the installations that you want to add to the BCD store. Use this option when you must completely rebuild the BCD.
Info copied from:
http://support.microsoft.com/kb/927392
