I'd wager a guess that maybe your really fat female had dropsy or was perhaps constipated. Did you feed them anything else but flake food? Sometimes really rich food too often can be a bad thing for their tummies.
If not, see if your fish perhaps resembled this one..
http://photos.wemm.org/supersized This one is a little extreme, but it gives you a general idea.
I know it's hard to remember back, but do you remember her scales sticking out at all?
In any case, guppies don't always get huge when they're pregnant. A normal pregnant guppy might look like any of these..
http://fins.actwin.com/fresh-pics/guppy-female.jpg
http://aquariumhobbyist.com/guppies/gravid.jpg
http://www.aquariumfish.net/images_01/my_baby_guppies_w360.jpg
(Note: I've never seen any of my girls get that big, and I also do not condone by ANY means putting a female in a breeding box like that.)
I'll give you the advice I give everyone, and the advice many seem to agree with.. since it is rather tricky to catch exactly when a guppy is pregnant, it's best to let the babies enter the world in a main tank. If you want to keep a seperate fry tank, try doing what I do and ladle-ing them out when you see them. When they're only a few days old, they're quite dumb and easy to catch in a ladle.. and also, it's much easier on the tiny babies than a rough net. However, the nets don't seem to hurt them. They're very... resilient when young.
As long as you give the babies lots of places to hide, and feed the adults regularly and well, supplementing them with live, frozen and defrosted, or freeze-dried food, they shouldn't go after the babies. Mine never seem to.
Besides, it's often best to expose them to danger a little.. because you certainly won't want to keep them all! You'll shortly run out of room in your house. :)
Good luck, and keep us posted.
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