See http://pastebin.com/UkFcVesT for "extra" git tasks being ran.

L4 clones the HEAD branch (usually master)
L7 and L8 bring in the HEAD's submodules.
L13 check's out the branchToBuild.

L14-L16 update the submodules to match the branchToBuild. But does not delete any submodules present in HEAD, but not present in branchToBuild.

The current process is:
clone, fetch, submodule init, submodule update, rev-parse, checkout, submodule init, submodule sync, submodule update

The correct proecess should be:
clone, fetch, rev-parse, checkout, submodule init, submodule sync, submodule update

I've forked the plugin on github and will commit a fix once I have the Issue #...