PHY Transmission - Arria II GX

Some PC network cards automatically disregard malformed packets or packets with invalid CRCs, so if you have a problem on the packet it could explain why you don't see it in Wireshark. Have a look at the driver properties and see if you can disable any hardware acceleration, CRC/cheksum calculations or error check. Some drivers also show error counters.

You could also try a loopback test, either by changing a register in the PHY chip or by physically connecting the RX and TX pairs on the network connector. Then you can have a look at the RX signals and check that what you receive is exactly what you sent.

Are you sure that the PHY negotiated correctly a gigabit connection? Are you using a DDR I/O block? In that case are you sure that you use correctly the high and low inputs and are sending the 4-bit words in the right order? Did you properly constrain the RGMII interface and does your design meet all timing requirements?