You are right. the drives should be planthy fast, but that is just one way of troubleshooting and making sure it is not the aray.
What program was the QT file you have imported created in and what codec are you rendering it too.
IE: If yo have an annimation codec file and you are rendering it down to DVCPRO50 then maybe you are introducing the artifacts when you are getting rid of the six lines of information in the rendered file.
FCP render settings? YUV, RGB, High Precision?
There are many variables here.
David