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You must be aware of the fact that before Wireshark gets its hands on an Ethernet frame a lot of other stuff needs to go right first. It is the networking hardware that handles the layer 1 and layer 2 stuff, i.e. on the cable the frame must have a proper preamble, start delimiter and then the destination MAC, etc. If the PSN in the FPGA isn't encoding this stuff right the network interface in the PC won't accept the frame and pass it up the network stack.
Have a look at the PC's network interface performance counters, to see if any of the error counters count up when the FPGA is supposed to send frames.
