I knew it had to due to line endings between Windows and Linux. Found this cool command from Waldo at http://www.macosxhints.com
There are many places where PERL is incredibly handy. This is one of them. You can use
PERL on the command line to change the line ending ( a '\r' (Mac) to a '\n' (UNIX) ):
perl -pi -e 's/\r/\n/g'
I have put an alias in my .bashrc file that looks like this:
alias fle="perl -pi -e 's/\r/\n/g' "
Now I just type fle
and everything works file. I use "fle" for "fix line endings," but
yo can use anything you want to.
Worked very well