Kona 3 and Apple ProRes 422 (HQ) capture problems

Okay, here's my story: trying to capture feature-length HD (1080psf @ 23.98 w/ 2ch embedded audio) off D5 tapes over HD-SDI through a Kona 3 into Apple's ProRes 422 (HQ) codec. I am using AJA's preset for this.

The problem: imaginary "timecode breaks" that stop the capture partway through at seemingly random points.

The machine: a Mac Pro Quad 2.66GHz with 4GB of RAM, AJA Kona 3, 4Gbit/s Fiber Channel RAID-5. This machine regularly captures 10-bit uncompressed HD with no problems.

Attempts so far: Using the AJA Kona 3 version 4.0 drivers (w/ FCP 6.0.1 on OS X 10.4.10) I was having the aforementioned problem. Captures would stop around 8 - 9 minutes, then 18 minutes, then 23, then 35. At that point I looked for solutions, and found the "2GB of RAM" problem on this board. We took out 2GB of RAM and tried again. We got to 54 minutes in before we had a break in the timecode.

At that point I tried a Capture Now, and crashed in (not the optimum solution since I'll now have to trim the file before delivery to ensure there are exactly 2 seconds of black before and after program). The first time I tried this, I got an hour and 54 minutes in (a mere 7 minutes before the end) and it dropped frames. Ready to pull my hair out, I put the 2GB of RAM back in and actually managed to get the whole thing on a second attempt.

Because being able to do a capture now would be better, I decided to update OS X to 10.4.11, FCP to 6.0.2, and the AJA Kona 3 drivers to 5.0. I'm currently running a test and as I'm typing this it hit a timecode break, but successfully "located it" and is continuing to run. I'm not sure if this will create any problems down the line for sure. In any event, I feel like I shouldn't be having these problems in the first place