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Sounds like you just printed on the wrong side of the transparency. The print side is coated with a special film to capture the ink. The other is un-coated so the ink will not stick, only puddle. You can also print on vellum with almost as good a blackout.
If you use transparency film with your inkjet printer set on high quality, the negative will be almost completely opaque producing finer edges. We use it in the screen printing industry to create the negatives for our masks.