It almost sounds like the particular .gif or .png images that you're trying to use haven't been properly saved to allow for the use of transparency.
Is it possible for you to share this logo that you're attempting to use with us? You can send it to (email@example.com with the subject "Transparent area in logo turns black". Once you've sent the image in, please comment below and we'll look further into this for you.
Please let us know if you had any further questions.
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