Hi Steven,
There are a couple of known issues with Git submodule checkouts. Would it be possible for you to raise a support ticket at support.atlassian.comand attach a Bamboo Support Zip (Bamboo Administration >> System >> Atlassian Support Tools >> Support Zip >> Create) to this issue? This way we can see what kind of checkout you are performing and what auth you are using and investigate further.
Thanks
Turner
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