That likely means that the publish over ssh plugin is setting an environment variable which alters the behavior of command line git, or is setting an environment variable which alters ssh behavior, and the ssh invoked by command line git is affected. The publish over ssh plugin would need to alter how it is setting environment variables to only affect its own ssh invocations.
You could test that theory by enabling JGIt as an implementation ("Manage Jenkins" -> "Global Tools Configuration" -> "Git" -> "Add Git" -> "jgit"), then modify one of the jobs to see if JGit is affected by the same changes from the publish over ssh plugin.
Does the problem only occur in jobs where publish over ssh is used, or is it in all git use throughout the entire system once publish over ssh is installed and configured?
That likely means that the publish over ssh plugin is setting an environment variable which alters the behavior of command line git, or is setting an environment variable which alters ssh behavior, and the ssh invoked by command line git is affected. The publish over ssh plugin would need to alter how it is setting environment variables to only affect its own ssh invocations.
You could test that theory by enabling JGIt as an implementation ("Manage Jenkins" -> "Global Tools Configuration" -> "Git" -> "Add Git" -> "jgit"), then modify one of the jobs to see if JGit is affected by the same changes from the publish over ssh plugin.
Does the problem only occur in jobs where publish over ssh is used, or is it in all git use throughout the entire system once publish over ssh is installed and configured?