I have no experience with the GS2, but use a 332 and have connected NEMA to many boxes.  So some suggestions:

1.  Don't try to output TSIP and NEMA from the same port.  Leave port A on TSIP and use port B for NEMA or get NEMA from the serial port on the NAV2.
2. Again not Familiar with the GS2, but I highly doubt it will need RTS/CTS.  Set the NEMA port for the correct baud rate and 8N1.
3. Set the NEMA output for 1 Hz (or 5 Hz if the GS2 need fast update), not ASAP.
4. I would expect that the Null Modem will be needed.

Not that it makes any difference, but which GS2 display are you using, the 2600 or 1800?

More than likely having TSIP and NEMA on the same port is confusing the GS2.  I would send it a clean NEMA string.