I get the same error here using beta 2 of the software and vista 5456.
First of all, using partly your software and some guides I found on the internet, I restored my XP partition to booting using XP only (bootsect /nt52 <driveletter>). But I noticed that the files BCD and BCD.log were in use when I had booted to XP using the Vista bootloader so I couldnt copy or access them. after booting with ntldr and boot.ini (the old XP way) I moved the boot folder and bootmgr file to the vista partition and used bootsect to set the vista boot sector on the vista partition. Everything worked and I booted and all, but I noticed the files were in use again. I gave myself full permission to the boot folder and all its files and the bootmgr file. However, whether launching cmd with admin permissions or launching vista boot pro, I get errors that that the BCD registry can't be acessed. Bcdedit say that the file doesn't exist, but that can't be true because I can see the files in explorer and know that I couldn't boot without them, and also, it says access denied when run in non admin mode.
Ok,whew, now that I've said all that, can you help me figure out what is acessing these files and how to solve the problem?