With Qsys and SOPC_Builder on Linux platforms, when adding custom components, error messages about missing top level module or multiple modules can be caused by the first line of /etc/issue being written into the PLATFORM tag of the temporary xml file. (See discussion on quartus_map terminates unexpectedly). This results in a parse error whe reading the xml file to create the interface.
By default the first line of /etc/issue contains non-printing characters, actually command sequence to clear the screen on boot up.