I'm using a Dual 2.7 G5 with the latest updates for Tiger and Quicktime. I've got 4.5 Gb of RAM, a SCSI RAID array and the AJA Kona LS video card. I'm getting random faulty frames when playing back video from FCP 5 timeline, exporting Quicktime or M2V files from FCP, rendering m2v files in Compressor, and also they seem to appear when I bring a Quicktime file to DVD Studio Pro to encode it there. After Effects does the same thing sometimes, but not nearly as often as the others. In each rendering the problem appears in different frames. As they also appear when I'm not using the Kona card for playback, I don't think the card is the issue. What else could it be besides faulty memory?
Most likely its a problem with your RAID, or a codec/driver conflict. Remove all codec's and drivers except the ones that are installed by OS X and by AJA for your card. Make sure your RAID is not full and is fast enough for what you are doing. You also should do a search for similar problems on the Final Cut Pro forum and the AJA Kona forums as you might find something usefull to help narrow down the issue. Finally, AJA has a pretty good FAQ on their website that can be very helpful as well. Make sure you system meets their requirements (see the compatiblity pdf on their site).
Oh, one final thought. Make sure your card's firmware and the drivers are the latest versions.