Yes it is a bit confusing, but it should talk to the right device...
The GPS Port is emulated as an UART1 device inside paparazzi, zo that it can handle all the normal paparazzi code.
What I advice you to do is to telnet in the device and stop the ap.elf and start it yourself so that you see the printf output. Normally when you enable the ublox ucenter module it will output at which baudrates it tries to connect to the GPS to set the correct settings. You could also enable some more printf's inside the ubloc ucenter module if I'm right. End else enable the printf's inside the uart code of the omap arch, then it will output all the informations end to and from the gps.
Hope this helps!