[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