There are several things you can check to fix this problem:
1. Is the file you are running an 8-bit TIFF file?
2. Is the file a single-layered transparent image? (meaning it does not say "Background" on the layers tab in Photoshop)
3. When saving the file after creating the transparent background, are you checking the box that reads "Preserve Transparency"?
Please check these items and if you are still having problems, we can help.