I put in this code temporarily:

       GPIOEzInit(LED1);
    GPIOEzInit(LED2);
    GPIOEzInit(LED3);
    GPIOSetOn(LED1);
    GPIOSetOff(LED2);
    sciSetBaudrate(scilinREG, 110);
    sciSetBaudrate(sciREG, 110);
    while(1){
    GPIOToggle(LED1);
    sciSend(sciREG,38,"Starting a test on the SCI register\r\n");
    GPIOToggle(LED2);
    sciSend(scilinREG,38,"Starting a test on the LIN register\r\n");
    }

The GPIO routines are my normal driver routines.  The sciSet and sciSend are the HALCoGen routines not using any interrupts or anything else.  Note that I set the baudrate to 110 (R-e-a-l slow!) and sent 38 characters.  That it, it should take about 3.8 seconds to print.   And indeed the light pattern changes at a rate of approximately every 4 seconds.  

 I have a terminal connected to PC104 pins 88 and 92 and set for 110 baud connected and at first saw nothing.   Then I reversed the rx and tx pins and.....

SO!  Either I have the colors wrong on my serial-to-USB connector, or they are backwards on the blinky board.  Will figure out which next, and then try higher speeds.