Here's the file that is causing the problem.
 
It starts with the with the 3-byte order mark and each line ends with with CR/LF except the two lines with character codes > 128 which end only in LF. When I open the file in Windows Emacs, each LF is preceeded by an additional CR so the lines with CR/LF end in CR/CR/LF and lines that end in LF end in CR/LF.
 
If I start emacs with the -Q option, I get the same result. Normally I start Emacs by running the runemacs.exe. I'm running on Windows. (I'll check the problem on Linux once I get the file there also.)
 
Thanks,
 
Henry.