I've encountered this problem too, I think, on a Mac slave using SSH:

Fetching changes from the remote Git repository
Fetching upstream changes from g...@github.com:proj/repo.git
using GIT_SSH to set credentials jenk...@github.com
Checking out Revision 370b0a3e37251b4a4898134a073c61e5624445f7 (origin/release)
FATAL: Command "git submodule update --init --recursive" returned status code 1:
stdout: Cloning into 'subrepo1'...

stderr: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Clone of 'g...@github.com:proj/subrepo1.git' into submodule path 'subrepo1' failed

hudson.plugins.git.GitException: Command "git submodule update --init --recursive" returned status code 1:
stdout: Cloning into 'subrepo1'...

stderr: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Clone of 'g...@github.com:proj/subrepo1.git' into submodule path 'subrepo1' failed

	at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1086)
	at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1063)
	at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommand(CliGitAPIImpl.java:900)
	at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.submoduleUpdate(CliGitAPIImpl.java:570)
	at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.submoduleUpdate(CliGitAPIImpl.java:551)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at hudson.remoting.RemoteInvocationHandler$RPCRequest.perform(RemoteInvocationHandler.java:299)
	at hudson.remoting.RemoteInvocationHandler$RPCRequest.call(RemoteInvocationHandler.java:280)
	at hudson.remoting.RemoteInvocationHandler$RPCRequest.call(RemoteInvocationHandler.java:239)
	at hudson.remoting.UserRequest.perform(UserRequest.java:118)
	at hudson.remoting.UserRequest.perform(UserRequest.java:48)
	at hudson.remoting.Request$2.run(Request.java:328)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:695)

Putting a id_rsa file onto the slave fixes that slave. However, we've got plenty of slaves, and plenty of jobs that run on them, so it would be a lot easier for us if it did what it says on the tin. Vote cast.

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