Dave,
Thank for your reply.
Yes, i did the initial photo alignment (I've tried various accuracy settings from low to high, I don't know if it matters).
The targets were plastic boards containing 2 white and 2 black squares but as you said, the black squares are not perfectly black in the pictures (and the white ones aren't perfectly white either). To increase the contrast during photo capture, we added some dark margin around one of the targets (using dark adhesive tape) - no effect. I find it hard to increase the contrast further without any postprocessing.
You can download another set of photos (taken with Phantom 3 Adv from 50m AGL, GSD around 2cm):
https://drive.google.com/open?id=1wYmVpuSdtsKpBXeW9TbHjESR8v_akxRBThis set of photos covers 2 targets (with and without dark adhesive tape around it) - although both targets seem pretty similar, only one is being detected automatically (the one away from the railroad, without adhesive tape margin).
These pictures are generally much darker, but the black areas on the targets are still just dark grey, so I don't know if it's possible do achieve higher contrast.
The photos were taken using Pix4D Capture app, which I belive automatically sets all exposure parameters and doesn't add any color corrections/filters to the images.