Hi again Willie,
I've now taken a look at the samples you sent me, and was able to reproduce the issue. It does seem that it has to do with the properties of the PDF itself, i.e. some part of how you are scanning them.
I opened up the problem PDF in a PDF editor and inspected the page set up: note the preview, as well as the Page Size Right and Bottom values, and the Contents size Right margina and Bottom margin values:
When I changed these as follows the PDF uploaded normally, and the first page thumbnail came out fine:
Now, given that the first page is a single page scan but the rest are side by side pages, I am not sure what the correct SCANNING page size should be - only that making these changes worked for AtoM's reference image, and that this confirms that the issue is with how the PDF's technical metadata is currently set. So, I think you will need to compare the two a bit more closely locally and make some adjustments to your scanning procedures based on what you find.
I hope this helps!