This bug makes the synthetic history generated by SourceTree incompatible with other subtree users. The root cause seems to be an extra "-n\n" in the commit messages generated by the embedded version of Git.
Steps to reproduce:
1. Clone this repository: https://bitbucket.org/jennings/sourcetree-subtree-commit-message-bug
2. Set SourceTree to use the embedded Git (version 126.96.36.199)
3. Use "Add/Link Subtree" to link the "sub" directory with a remote repository.
4. Push the subtree.
5. Set SourceTree to use the system version of Git (tested with version 1.8.5)
6. Push the subtree.
The subtree created using the embedded Git has a head commit ID of 6e92039. The subtree created using the system Git has a head commit ID of 329f350. Resultant repos can be seen here:
Both branch head commit IDs should be 329f350.