Hi all I have a similar problem, I have 6 hard drives, 4 in a raid 0 (2x80 gb for Vista Ultimate 64 & 2x250 for Applications and Games), 2x500 gb for backup and storage.
The problem I am getting is after every restart/shutdown I get the BCD error. I have to take the 2 500gb backup drives out (disconnect power), then boot from vista disk, repair the errors with 'bootrec/fixmbr, fixboot and rebuildBCD' and then reconnect HD's and everything works till the next boot. I thought I had fixed it a week ago but the errors have started again.
I have used EasyBCD, I have used Vista repairs, but for some reason the BCD is not working after shutdown. Any help would be truly appreciated. Thank you for yours time.
Addendum:
More information, I have just gone through the repairs again and left all the drives connected. I now notice that C: and D: drives are not there? (I presume that C: & D: are my DVD drives? When they are set to Y and Z in Vista) My Vista is on E: yet once in Vista all drives showing in the right place i.e. Vista C:\. I went into E:\ (under the Vista Repair program) and bootrec/Fix... but it failed on the fixboot and rebuildBCD. I have tried EasyBCD again then gone back into Vista repair and the same issue still stands. Has anyone got a good idea please.
Thank you for your time.