All of our developers work on windows machines and build is done on Linux.
In order to conform the true way we decided to normalize line endings and follow
I did had the same problem once. I can only give you one advice.
For me its not the work of a VCS to manage our line endings. Its the job of the developer or the IDE. So normalize your line endings once and after that switch the line endings on the windows machine IDEs to Unix-Line-Endings and be happy again. Thats what solved our problems.