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Defining a project-specific commit template has no effect (at least with EGit), even if the project is associated with a task repository. The global template defined in preferences is always used.
Are you using the staging view?
You're right, this bug only seems to affect the EGit staging view. When using the commit dialog it works correctly. Moving to EGit/Mylyn.
There was already a bug for this... I think. *** This bug has been marked as a duplicate of bug 348744 ***