I've installed an update of SourceTree yesterday, and this morning I happened to have an issue related to line ending handling.
A detailed explanation of the problem and solution is available at http://stackoverflow.com/questions/17362377/binary-equal-files-show-as-modified-unable-to-revert
Summarised, I think SourceTree has mixed configuration of the eol extension with configuration of the old win32text extension. Would you be able to verify this in your codebase?