Error Opening BCD Registry


I have a dual-boot Vista x64 and Grub/Linux (Debian/Lenny) system. Currently I have both systems booting up fine. Both OS's are on the same HDD in a Vista 1st configuration. The Grub bootloader is on the Linux partition (hd0,1), however the MBR is altered by Grub to select what OS gets booted.

The main problem is that I can't install Vista SP1 or SP2 on the system (apparently because of the Grub modified MBR). I was hopeful I could use EasyBCD for booting into both OS's, and allow Vista SP updates. However, while in Vista, starting EasyBCD I get "The boot configuration data store could not be opened. The system cannot find the file specified". From the documentation, it seems like EasyBCD has tools to repair/fix BCD issues, but it won't startup without finding a valid registry store. How do I proceed? I am trying EasyBCD 2.0 Beta (v 76?)
Thanks for the quick response. That's what I suspected and have the repair ISO downloaded. From there I assume I'll lose ability to boot to Linux and I can simply configure EasyBCD to remedy that?
Started working on this and have found that I need to use (at least) step 3/manual recovery. Unfortunately, my Vista 64 installation, recovery disk and the recovery CD image downloaded from a NeoSmart link, all do not contain bootsect.exe. I see one is installed with EasyBCD. But I've seen it indicated elsewhere that there is one for 32-bit and another for 64-bit (not sure if that is correct). Will the NeoSmart installed bootsect work ok for the Vista 64 boot sector?