When you installed Vista, it put its boot files on the "system" partition (XP) and automatically dual-booted. That's standard MS design for new OS following older OS.
When you cloned Vista to a new HDD, the UID in the BCD on the XP drive still points to the previous HDD (UID describes the physical disk ID and the start location of the partition).
Delete the Vista entry from the BCD and add a new one, pointing to the new Vista partition.
Use EasyBCD 2.0 "Backup/repair BCD" > "Change boot drive" and point it to your new HDD when it asks.
Change the BIOS to boot from the new HDD , then reboot into Vista
You should find that the new Vista is now "active" "system" "boot" in the Disk Management flags, and that you are now free to format and reuse for any purpose you wish, both the old partitions.
delete any redundant entries from the BCD and when you have only Vista left, you will no longer be presented with a boot menu.