The initial git clone will behave differently than normal because git doesn't behave consistently across empty/non-empty repositories. Subsequent build attempts, even after making the repository non-empty, end up failing with:

ERROR: Problem fetching from origin / origin - could be unavailable. Continuing anyway
ERROR: Could not fetch from any repository
FATAL: Could not fetch from any repository
hudson.plugins.git.GitException: Could not fetch from any repository
at hudson.plugins.git.GitSCM$2.invoke(GitSCM.java:735)
at hudson.plugins.git.GitSCM$2.invoke(GitSCM.java:702)
at hudson.FilePath.act(FilePath.java:753)
at hudson.FilePath.act(FilePath.java:735)
at hudson.plugins.git.GitSCM.checkout(GitSCM.java:702)
at hudson.model.AbstractProject.checkout(AbstractProject.java:1116)
at hudson.model.AbstractBuild$AbstractRunner.checkout(AbstractBuild.java:479)
at hudson.model.AbstractBuild$AbstractRunner.run(AbstractBuild.java:411)
at hudson.model.Run.run(Run.java:1324)
at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:349)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:139)

This should be easy to reproduce and I strongly suspect it's just about the difference in which git initializes .git/config for the empty/non-empty cases. I'm not familiar with hudson and it's git plugin enough to make any concrete suggestions as to how it should be handled in this particular case