What is the switch environment look like? Or are you directly connected to the storage? I assume you have two ethernet switches. Do you have only one pNIC assigned to each vmkernel port group? Or are both assigned, but in an active/standby configuration? Are you LUN masking on the EQL box?
I assume the W2k8 server is physical? If so, are you running any multi-pathing software on it? How many NICs in the box? LUN masking?