Dear Michael and Dave,
The problem is definitely on the account of a missing “-native” structure. As repeatedly noted in the documentation the -native flag is required by FlexPepDock. It is used for RMSD calculations, as michael mentioned you can input the starting structure (same one you use for ‘-s’) or a different reference structure (like the actual solution, or a different model, etc…)
Regrading discontinuous numbering, this should pose no problem, Michael, if you can reproduce the scenario please send us the cmd-line and PDB and we’ll check it out.