Run diskmgmt.msc from Start.
When you install multiple Windows OSes, and do not take
precautions, one partition will be marked "System" and
another one marked "Boot". And when that happens, you can
be in for surprises, if one of the disks is unplugged,
you delete a partition you do not think is being used,
and so on.
While your problem can be fixed, it requires a knowledge
of the boot process. And even then, you will need to keep a
diagram somewhere, of which partition is "controlling"
things, so you do not accidentally remove a dependency from
files such as the Windows folder. Microsoft switched the
terms, just to confuse.
The partition that does not have the boot.ini, should appear
in the boot.ini of some other partition, as a new entry at
the bottom of its list. If you boot the disk with that
boot.ini on it, then you may see the orphan OS as a
boot option. While something like "bootcfg /rebuild" might
be suggested as a means to glue things together, that command
can also cause more problems than it solves. So rather than someone
just giving you a recipe, really you have to become
a rocket scientist first. Like later, you might
decide to just delete some partition (thinking, it is
no longer used), only to discover that the boot.ini
was running your whole computer.
To avoid this on my computer, my policies are:
1) When installing an OS, unplug all other disks but the
one getting the install. This prevents the installer crafty
logic, from entangling two disks and making them dependent.
2) Install no more than one OS per disk. Now, there is no need for the
installer logic to try to make one partition "in control",
have the only boot.ini, and present a menu to "manage" the
other OS partitions.
3) To change OSes, I select them from the BIOS popup boot menu
(F8 or F11, depending on brand of computer).
You're certainly allowed to relax those rules, but you have
to become a rocket scientist first. Bootcfg might be able to
fix it, and maybe some other helpful person here can guide
you to a successful conclusion.