Lines on page when redaction applied

I get files from another department that I then have to redact. For some reason, when I apply the redaction marks, I get "comment" lines from every redaction mark down to the bottom left corner of the page.

I've found a workaround by inserting an empty watermark and than preflighting (Flatten Transparency) before applying the redaction marks. This keeps the lines from appearing but changes a 40pg 1MB file into 5.5MB.

Any idea how to resolve this? The department from which I get these files use a high-speed scanning/generation system. The files indicate they are created with Amyuni PDF Convertor (PDF Version 1.5).