I have seen where the Multiplexor controller on the bay slows the performance down with controllers that have better performance on others. Likely due to what you reference. Firmware updates for the bays have changed this. Very similar to what I see with USb3 multibays. However the caching policy is at the E-Sata controller level and that is where the largest performance difference is made. I have also seen this with onboard Intel controllers and raid. They often change their caching policy and the raid 0 performance changes because of that. Sonnet just seems to have a much better caching policy than the other controllers.
Eric-ADK
Tech Manager