I'm not sure if I can help but I am attempting a similar project.
I have a ublox LEA-6 module but it is inside a antenova module (part number M10382). I have a Ethernet Arduino with a shield on it that contains the antenova GPS module. I find that I can connect to the GPS module using U-Center over the shield USB port. I can also connect to the GPS module from the Arduino using Software Serial on pins 5 & 6. I keep all the baud rates to 9600 N81 for testing and it does work.
I cannot seem to get the serial link to the Arduino running unless I have the USB connected to to the shield for some reason. Have you tried connecting both ports?
I also cannot figure out how to get the GPS module to start up under serial control only. For some reason it requires the USB connection.
You can see my project here:
http://www.seti.net/Cosmic%20Rays/Engineering/engineering.htm
The Arduino code that seems to work is
/*
Software serial multple serial test
Receives from VS 2012 app (hardware serial), sends to ERGO Shield (software serial).
Receives from ERGO Shield (software serial), sends to VS 2012 app (hardware serial).
The circuit:
* RX is digital pin 5 (connect to TX of ERGO Shield)
* TX is digital pin 6 (connect to RX of ERGO Shield)
*/
#include <SoftwareSerial.h>
SoftwareSerial mySerial(5, 6); // RX, TX
void setup()
{
// Open serial communications and wait for port to open:
Serial.begin(9600);
mySerial.begin(9600);
while (!Serial) {
; // wait for serial port to connect. Needed for Leonardo only
}
Serial.println("G o o d n i g h t m o o n!");
}
void loop() // run over and over
{
if (mySerial.available())
Serial.write(mySerial.read());
if (Serial.available())
mySerial.write(Serial.read());
}