Converting 59.94 to 23.98?

I've cross posted this to the HD forum, but I was hoping some of you Varicam pros might help shed a little light on this issue for me. I'm editing a project that was shot on a Varicam at 23.98 in a DVCPro HD sequence in Final Cut. A few clips need to be cut in to the sequence that were recorded on a Varican at 59.94. I've run the clips through after effects and rendered them out at 23.98. Most of the footage converts perfectly, but some of the scenes have a very strange strobing effect to them. I've tried a few different settings in AE, but nothing has worked. What could be causing this problem and why would some footage convert cleanly and not others? The original footage was captured with a Kona HD card using the Blackmagic 10-bit codec @ 59.94. The footage plays back fine when monitored through my Kona 2 card at 59.94, but select clips are a problem when converted to 23.98 in After Effects. Any information or help is greatly appreciated.

Thanks,
Mike