Printed your file on a 7970 and scanned it on a B8055 (don't have a 65 to use but they are the same device clocked to diferent speeds)
1.Scanned at the 8055 with default scan settings and I don't see the boxes, but the quality is terrible due to using default settings (XeroxTechGuy.pdf)
2. Same scan done again with the text searchable, still no black boxes, which got me thinking, because if there was handwriting on the pages, OCR/searchable will trip and fall all over the place and can cause massive weird issues. You never mentioned it, so maybe I am jumping at shadows there. (XTGocr.pdf)
Your 2nd file can't be retrieved, not sure where it stalled
Possibly related, your firmware is quite old, but since a FujiXerox also has the issue it may not be an issue, having said that, I would still update it.
Pretty sure your 2nd DNS server isn't right since it shows a 192.168.x.x address when the machine is on a 10.40.x.x LAN
Server Fax/Embedded Fax/Internet Fax are all disabled on the MFP, are you using Scan To Email for the job you are having the issue with?