Here is some more information about what is happening:
I have a relatively simple PDF. It is located at:
https://drop.atti.com/drops/d3dd5a4b73c5ec42b4250c06fbe1621
As you can see, there is a colored circle, and inside it is a white icon. These were created by layering images.
Using jPedal getPageAsHiRes(), the image is converted to a PNG. The PNG file can be found here:
https://drop.atti.com/drops/b40ed6c1807bde637919f415ae1e6397
As you can see, the white icon was converted to transparency in the conversion.
This behavior does NOT happen with a previous jPedal version that was shipped with ColdFusion 9. It occurs with the version that ships with CF10 as well as the CF9 Hotfix version.