I installed the MBP 2011 software updates released on 5/5/2011. This seems to have fixed the problem.
I was able to copy over 60GB to my Seagate GoFlex drive using the Seagate Firewire 800 adapter that previously exhibited the problem.
I did this by several tests involving 11GB disk images and one test with 14GB of disk images. For almost all the tests the entire copy completed at 50GB/s.
However, when trying to copy 14GB, after about 11GB had been copied the transfer slowed to 4GB/s. It continued to copy, but much slower. At the same time, CPU utilization went up dramatically, to where finder was using a complete core, and the machine got warmer. At this point the destination drive was nearly completely full (less than 5GB free on a TB drive) so fragmentation may be the cause of the dramatic slowdown.
I think this confirms my hypothesis that it was a bug in interfacing with some FW800 controller chips and has been fixed by the software update or the firmware update that was released today.
Notably, the FW adapter was quite warm, and the issue may be due to it overheating, and apple has simply put in a work around to detect this.