When the eclipse plugin applies the preprocessing to a file, the carriage returns are modified to whatever platform you are operating on. This plays havoc when integrating with a repository such as svn as even when preprocessing is set back to the default, any files with preprocessing are still shown as being modified, and worse - checked in as being modified. Instead, antenna should preserve the existing line breaks which shouldn't be hard to do.
(Apologies if this is now added twice, I previously reported this bug but can no longer find it on the list)