Minimize Search Distance in Image Registration?

Hi there. I have thousands of images that are slightly misaligned and I need to get as perfectly registered as possible. They are thermal images and in each image are 5 reference targets that should make the registration easy, but I can't figure out how to get Matlab to play along. Here is an example of an image:

When I put this image and another in to the registration app it sometimes picks up the black points, but when it does it tries to match them to opposing corners:

My first thought is if I can define a maximum search radius between points then I could improve this registration, but I don't see an option for how to do that. I have roughly 250,000 of these that I need to do so I can't fine-tune the parameters on a per-image basis.

Anyone have ideas? I'm very new to MATLAB. The example r-jpgs are attached.

Thanks in advance.