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I would guess you're seeing a side effect of another bug. Instead of using ${BRANCH} in the Branches to build field, trying using the value of that variable (as a test). If the value of that variable is honored, then you've encountered a bug that that variable expansion does not seem to be applied to the values entered into the Branches to Build field.
If that doesn't allow you to checkout submodules, then I'm not sure of any other alternative.