USB ports on PCs typically are on a single internal USB hub, so the total bandwidth is shared amongst all the ports. By the time you take in to account the shared bandwidth, the read and write delays of the two drives, any conflicting data from other USB devices, and Windows latency, that could explain why the transfer rate is so low.
However, some PCs have two internal USB ports connected to two internal hubs, and if you can get the two hard drives on separate hubs the transfer rate should go up significantly.