Are you sure they're both labeled "C"?
Long story made short: A friend had the identical problem (Except the
phantom drive was "D".)
Tried everything. Solution:
Disable the phantom drive with tweakui, use fdisk from a command prompt to
delete the phantom partition. Fdisk would not delete the drive until it was
disabled with tweak.
I'm not sure this will be useful if the drive is  "C", but take a look at
what fdisk shows anyway.
Good luck.
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****************

   A friend of mine just reformatted his hard drive and installed win98 SE,
and now has two C: drives showing up in windows explorer but not My
Computer. I originally thought maybe somehow, he made a shortcut to it
somehow... but it's not showing up like that. When he puts something in
one, it shows up in the other. Anyone ever heard of this and how would one
go about fixing it?

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