My best guess for a Sunday is that you are missing frames while you are
busy writing your flash.
Your Ethernet chip can only hold a limited number of frames and if you
don't empty it frequently enough, or your driver runs out of pbufs to
store incoming frames, you'll lose them.
Try to enable breakpoints on key places, enable statistics, I like to
move pins when entering and exiting critical regions and watch the flow
on a Logic Analyzer (cheap USB).

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