Did you perhaps do an image copy to the new disk, so that
the disklabels are identical?
The boot disk is identified by comparing the disklabels
with some data passed in by the bootloader, to avoid all
these BIOS numbering problems mentioned in previous
replies.
If this is the problem, you should have got a message
like "warning: double match for boot device (wd0, sd0)"
during boot.
A small change to the disklabel, eg in the "label"
string, should help.

best regards
Matthias