Can you set your vision system to only find the outline of the fiducial? I have seen this in the past, the reflection of the domed solder scatters the light causing it to look like a through hole. By setting the vision parameters (if available) to only find the outline it will ignore the dark center spots.

As others have mentioned, you can try SMOBC for the fiducials. I have had to do that was well due to limitations of the vision system.

Regards,