The problem is if fread() is called multiple times, then UnicodeConvertor->convert() is called multiple times, which causes m_pNewBuf to point to the last read in chunk. Then after the entire file was loaded, getEOLFormatForm(UnicodeConvertor.getNewBuf(), ...) was being used which was only trying to detect the EOL mode from the last read in chunk. If this last chunk started with \n then the file was detected as Unix line endings. The file linked from issue #1002 happened to have just the right situation where this occurred.

I am not very familiar with different types of file encoding and never have to deal with them myself. I tried to test this as well as I could but by all means please thoroughly review this. Thanks :)