find in "save as" or use newline madness plugin
By default, Gedit maintains whatever EOL format the file had when opened. You can change that when saving the file if you use the "save as" option and choose an alternate EOL (Unix/Linux = LF, Classic Mac=CR, Windows=CR/LF). The plugin "NewLine Madness" provides an indicator of the current file format in the status bar, as well as a function under the Edit menu to change the format.
You can then choose whichever file format you prefer with which to maintain your files across systems.