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Martin,
Assuming that the images are aligned:
1. Crop the first image
2. Save the first image
3. Do not close StarTools.
4. Load the second image
5. Go to crop module and just click Keep. The cropping borders from the first image will apply and the images will have identical sizes.
6. Save the second image.
7. Process each image before using Layers module.
You can also fully process the first image and then move to the second image but the key is not to close ST so it keeps the cropping borders. Alternatively you can find the cropping parameters from the log file, or just write them down.
Also, as already said, if you bin the images you must use the same binning for both images.
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