This problem relates to a System Generator design that is organized as multiple subsystems, that is with a "multiple subsystem generator" block and underlying system generator blocks. If the options for the NGC netlist in any of the underlying system generator blocks are set to disable writing a clock wrapper, the following error occurs and the combined netlist is not produced:
".. An error occurred while generating using the Multiple Subsystem Generator block."
Currently you must enable the clock wrapper for all subsystems when using the Multiple Subsystem Generator Block to generate your design. This issue has been addressed in the System Generator for DSP 9.1 Software.