You may need to fix the MBR (master boot record). In the MBR it still wants to boot from the first partition. You'll need to create a new one so that it sees the your second partition as the first one.
You should delete the first partition, move Vista 64 partition to the start of the disc (OS partition should be near the start of the HD as much as possible), a free solution like QPart can do this. Then you can use the Windows repair feature with the installation DVD.