In Windows, I’m using the egit plugin freshly upgraded to the 20120613 version.
git status and git diff on the command line show the correct uncommitted changes.
In Eclipse the Project Explorer shows correctly the projects and files that have modifications.
UNFORTUNATELY:
If I right-click on a project and select Team / Synchronize Workspace it shows ALL the files changed.
If I right-click on a changed file and select Compare With / HEAD Revision it shows the entire file changed, I have to make it ignore whitespaces to show the actual relevant changes.
I have core.autocrlf=true in the global configuration, in my user’s configuration, and Eclipse Preferences agrees with this too. (I do not override it in the repo.)
The project comes from a git svn clone, if that matters. Normalizing all the line endings and committing back to the main project is not an option either. The problem is clearly not with git but with the egit plugin. And only in Team Synchronize, otherwise it’s working fine.
I’m actually trying to sell the idea of using git instead of Subversion, but if the Team Synchronization doesn’t work well, it’s a huge disadvantage compared to using Subversion.
UPDATE
In the latest version of the plugin the problem seems to be solved. I just migrated my workspace to Eclipse 4.2 (Juno), installed egit, and now Synchronize Workspace seems to work fine.
I’m not sure about this Q&A since it doesn’t aware about Eclipse, but I believe something there may be applicable to your case.