Just a hack suggestion, but have you tried running dos2unix or unix2dos on the files before or after the formatter to get the files in the right format?
Also, what editor are you using? I know I just wrote the blazemod vehicle part descriptions using vim and notepad++ on Windows, screwed up the commit sequence, pushed the mangled commits up to GitHub, pulled them back down to a Linux box, rebased them the correct way with git gui, and submitted them without any CRLF issues.
Now, I strongly suspect I’ve configured my notepad++ and vim on Windows to use Unix style LFs and forgot about it, but my second step would be to check if you can get your editor to do the right thing.