There is a difference in how files are stored on these two operating systems.

By default, when files are created on a windows system, the end of the file is marked with a ctrl-r and a ctrl-n. The user does not insert this, it is done automatically by the software. This is not the case in the linux/unix environment. The end of line in linux is marked only by the ctrl-n. When performing text processing, the ctrl-r will cause problems in the linux environment.

To see if your file contains ctrl-r use the linux command od. Od stands for Octal Dump and will display the contents of the file in various formats. In this case, you should run od -c filename. This will display each character in the file, with some special characters, like ctrl-r and ctrl-n proceeded by a slash.