It is described on page 3-3 of the tse user guide (http://www.altera.com/literature/ug/ug_ethernet.pdf), option "Align packet headers to 32-bit
boundaries (applicable to 32-bit FIFO only)".
This 2-byte padding enabled to align the 14-byte Ethernet packet to 32-bit boundaries so that the rest of the packet is aligned. The Interniche driver uses this to prevent from having to shift every word after the Ethernet header. This option can be turned off it you don't need it (but as said in the documentation in this case it won't work with the Interniche driver any more).