JB what multi-path provider and policy is currently in use for both solutions? I would imagine that the DIY box has the NMP provider and some form of DEFAULT "PSP". Is there a special PSP for the EQL or does it use the same one? Also you may be hitting some form of queue limitation on the EQL testing. I have found that there are almost too many layers to check queuing but here are the ones I focus on:
1. HBA Queue - ESXi default is 30 now, used to be 64 backin 4.x days
2. VMKernel Queue - not sure of default?
3. Device Queue (LUN) - Default is 30
4. Guest O/S Queue - Windows has a standard queue limit of 30 as well
If you see ANY of these queues maxxing out, your performance will never climb higher. Most of my testing shows that once you resolve the LUN queues by using more LUN devices in some sort of striped config, the other queues are mostly hardware limited. The HBA queue problem is usually fixed by adding more HBA's (or NIC's in your case). The VMKernel and Guest O/S queue problems are usually due to CPU or PCI limitations of the hardware.
Hope this helps!!