Using maven 3.0.3 and jbehave-maven-plugin 3.5.3, I am able to reproduce the problem above. I am using the maven command line client, not the embedded eclipse maven.
The problem seems to manifest itself only with the maven "site" goal. In this case the configuration section appears to be more or less inherited from the maven-surefire-plugin configuration?? This is true at least for the includes and excludes. I have no idea how this can be, but it is pretty easy to verify.
An "mvn test" runs fine, with configuration data injected as expected.
I think this issue needs to be reopened and looked at, there is definitely something funny going on here.
Actually, the Ant DirectoryScanner already has the SCM patterns excluded by default.
The problem of SVN files being included in the finder lookup doesn't seem to be reproducible - at least on command-line.
It seems though from thread on list that issue occurs withing IDE. So more details are needed to reproduce and verify (possibly a sample project).