[OT] RAID controllers blocking one another?

We have a machine that serves as a fileserver and a database server.  Our server hosts a raid array of 40 disk drives, attached to two3-ware cards, one 9640SE-24 and one 9640SE-16. We have noticed that activity on one controller blocks access on the second controller, not only for disk-IO but also the command line tools which become unresponsive for the inactive controller.   The controllers are sitting in adjacent PCI-express slots on a machine with dual-dual AMD and 16GB of RAM.  Has anyone else noticed issues like this?  Throughput for either controller is a pretty respectable 150-200MB/s writing and somewhat faster for reading, but the "blocking" is problematic, as the machine is serving multiple purposes. 

I know this is off-topic, but I know lots of folks here deal with very large disk arrays; it is hard to get real-world input on machines such as these. 


Thanks,
Sean