You probably need to send serial outputs to the serial-over-USB port, adding this to your initscript.cfg, after you have loaded a module with setmapping2:
setpar serout USB
Have a look here for more details: http://jevois.org/doc/UserCli.html
in particular, see section on "Serial communication types": JeVois sends two types of messages: log messages that provide information messages to humans (serlog), and output messages about what it sees and that are intended for machines (serout).
Then, each of these can be directed to either the hardware 4-pin port, or serial-over-USB port, or both, or none.
To select what goes where, you send instructions to JeVois, eg
setpar serout Hard # serout messages to 4-pin port
setpar serlog USB # serlog messages to serial-over-USB
setpar serout None # serout messages not sent anywhere
setpar serlog All # serlog messages sent to both 4-pin and serial-over-USB
In the code of a module, to send a message to serout, you use sendSerial(), and to send to serlog you use LINFO(), LERROR(), or LFATAL() and note that LFATAL() also throws an exception.