Version of InDesign? PDF preset used? What format of graphic? What PDF reader are you observing this in?
How does the INDD file look like if you turn on the prin preview inside InDesign?
I can replicate this problem but the solution is so convoluted that I hesitate to spell it out.
Go to Window > Output > Attributes.
Use the Direct Selection tool to select the image inside a frame.
Check to see if the image has been set to Nonprinting in the Attributes panel.
If so, I would image there is a black fill inside the frame.
But as I said, I sincerely doubt this is the problem.