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Yes, if you want to use the new version (1.3.0), then you'll need to stop using include/exclude paths/users.
The new version (1.3.0) still uses "git show" to compute "isRevExcluded" just as versions 1.1.25 and later did. In your case, you're probably best to stay with 1.1.21 until there is evidence that the problem is resolved.
The new version (1.3.0) is still in the midst of a refactoring which will allow it to use JGit or the command line interface. That refactoring has caused some instability and loss of functionality compared to 1.1.26. You may want to avoid the new version (1.3.0) until it stabilizes further.
Refer to JENKINS-17204, JENKINS-17242, JENKINS-17198, JENKINS-16941, and others in the git plugin bug list.