Just my two cents on the issue. I would need to take some time to test it out and/or read some RFCs.
Is the POP3 client setup to just download the headers and then goes and gets the full content later?
*maybe* your client is retrieving the first 655 characters part of the header and inserting a new line at 655. I believe there is a "TOP" command in the POP3 RFCs that allow specifying the number of lines to get along with the headers. Then when it gets the rest, Domino is just sending the 656+ and the client pieces it together.
I'm not saying it is not a Domino issue, just thinking about why that character.