What those errors means? Is the boarding receiving any data? Is it trying to process?

I just put them down to network communication glitches (the getwork times out or fails to connect). It all works much better if you install a Stratum PROXY server as an intermediate https://github.com/slush0/stratum-mining-proxy

As for your query about makomk_mod, I posted a reply at the main fpgaminer thread https://bitcointalk.org/index.php?topic=9047.msg1901149#msg1901149

Regards
Mark