If 'both' are changing, then your dual boot is almost certainly just booting the same installation whichever you chose.
Try disconnecting the first drive - if the second is an exact clone, it should boot on its own. The only problem might be what I mentioned - as the second drive has already been designated D: when booting from the first, its system drive will probably be D: (even with no C: present). But its registry will still be referencing C: for some items - so this may generate errors. Generally after cloning a drive, if you want the clone to work in the same way as original, you should disconnect the original before first time boot with the clone. This will let the clone establish itself on C:. Ie, its system drive will be C: - the partition its installed into - when you boot from it. Then when you reconnect the original drive, that drive's partition will take up the next available drive letter in the cloned installation (usually E: or F

. This will happen even if you use a boot mamager like system commander. So the idea is that whichever installation you boot from, its system drive (the partition its installed into) will be C:, and the other drive will have a different drive letter.
In your position I'd uninstall the system commander boot manager, clone the first drive to the second again (so starting 'clean'), then boot from clone on its own. Then reconnect original and boot from it (it wil automatically if its first in boot order). Then recreate the boot menu (you can use system commander - or just edit boot.ini on the first drive as per my earlier post, ie:-
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Home Disk 1" /fastdetect /noexecute=optin
multi(0)disk(0)rdisk(1)partition(1)\WINDOWS="Microsoft Windows XP Home Disk 2" /fastdetect /noexecute=optin
You should then have 2 independent copies of XP Home.