I’m not immediately clear on what your problem is. If you post the PDB and the options you used I’ll take a look at it.
I’m guessing there’s an issue with the fold tree. Try re-organizing the components of your complex in the PDB such that protein with the flexible tail is the last one in the PDB file. You don’t need to change the coordinates and probably not the numbering/chains – just make sure the flexible one is last. Let me know if this fixes it so I can update the documentation.