I loaded the file “BoxIssue.txt” using Multi-Edit 9.0e and there were no box characters. I also tried loading it specifying DOS, and then UNIX and there were no box characters, no extraneous characters at the end of any lines.
Loading the file as a Binary file I see it appears to use hex 0D 0A as line terminators, but it also uses 0D for newlines which are blank.
So my best guess is I modified the Remove_Boxes.s program to remove any hex 0D characters and then any hex 0A characters. Attached is the new file. You can load this file, compile it, then run it via or MACRO -> RUN and type in Remove_Boxes and see if it removes the boxes from your file.
You can also load your file with the boxes and specify Binary when you load it. FILE -> OPEN, and in the Type field (lower left) select Binary. Then scan for the 0D 0A indicating end of line and see if there’s some box character next to that.
You could also take a screen shot and post that here as an attachment in a .zip file as before.