We don't know enough about the situation to identify exactly what the issue is. Here are a couple things, though:
- Are speed / duplex's matched correctly?
- Are you oversubscribing the 3750E? This switch has a blocking switch fabric that could create issues. Look at the Cisco 4900 series for non-blocking models (better for high transaction, lossless environments like SANs)
- Are there switch bugs?
- Are there other devices connected to these switches? Are they on the same VLAN?
- What does the utilization look like on the ports where the SAN is connected?
There are lots of other potential issues as well. I hope this helps, though.