Can you open the unrecognized scans window, click on "Preprocess" and post a screenshot?

Ok. Here is the screenshot.

Thanks.
You can see that the corner marks are correctly recognized, but some binary boxes (in the header) are a little too light, so that they are erased by the B&W conversion process.
Maybe you can tweak the Preferences/Scan/Scans conversion/Black&White conversion threshold parameter? Try a little higher value.