What is the problem?. what is the difference between PC and FPGA-based board?
You have the data and test/setup, you tell us what is the difference!
Maybe then the problem can be guessed.
Else you have to build a test setup for debugging>
1. FPGA1 to FPGA2 : Have a frame generator and checker built inside your design implemented with FPGA1. Have a frame loopback mechanism inside your design in FPGA2. Make a test such that all frames sent out from FPGA1 are loopbacked from FPAG2 and verified in FPGA1 as they are received. Test this in hardware. e.g. even if 1 loopbacked frame has error then light up an on-board LED or something like that.
2. FPGA to PC - You can use Wireshark to monitor the received frames.
That's the best I can help you for the info you have provided.