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For me, the solution was to update the sub-modules in a batch script prior to the build. I created a new SSH keypair and saved the public key to the bitbucket user (keypair saved to C:\users\USERNAME\.ssh) Then I ssh'd into g...@bitbucket.com to generate a known_hosts file. Since Jenkins runs as a Windows service, I copied my SSH keys (id_rsa, id_rsa.pub, known_hosts) from C:\users\USERNAME\.ssh to C:\Windows\SysWOW64\config\systemprofile\.ssh.
After that was all sorted, I added a build step (needs to be the first build step). I created a Windows batch command that contained the following entries:
git config submodule.SUBMODULENAME.url g...@bitbucket.org:SUBMODULE/DIRECTORY.git <-- ssh access url
git submodule update --init --recursive