Reverse Telecine - clips behave differently in timeline.

I'm in the midst of a very time-consuming workflow that seems to be getting more so with every step. I have 1080i60 footage shot with a Sony Z1U in 29.97. We need a film out and we're also using HVX 24p footage so I MUST set up a 24fps timeline and I MUST reverse telecine on all the Z1U clips. We're talking over 250 tapes. I've spent the past 4 weeks Recompressing the HDV Z1U footage in Media Manager to Apple Intermediate Codec as it's the only way to get those clips into Cinema Tools and perform the reverse telecine. Of course batch reverses don't work because CT does not automatically recognize the A frame on these clips. So I manually find the A frame for thousands of recompressed clips and then reverse them.
Now comes the problem: I did some stringouts over the past few weeks with these clips without fail. But now I'm assembling a rough cut of the feature and clips which appear properly reversed in the viewer (meaning they're in 23.98 and advance movement with every frame advance) don't behave the same in the timeline (meaning there is a freeze frame at every fourth frame).
this is usually the behavior of clips which have been improperly reversed, but the fact that they are fine in the viewer and that they've already been manually reversed doesn't add up.
a QUICK FIX is what i need. please help. Thank you

FCP 6.0
OSX 10.4.10
2 x 2.66 Ghz

I'm noticing a pattern which is disconcerting:
During this work flow, overnights I've been batch Reversing in CT hoping maybe a fifth of the clips would be successful. During the day I check all the clips, using the viewer window as the litmus. If the frames advance smoothly, I assume it works and file it accordingly. if there is a freeze at every fourth frame, I assume it doesn't and manually reverse it by stepping to an A frame in CT. It happened that about 20-25% we're good which validated my theory that, since there are 5 frames of video a second, about a fifth would be parked on the A frame at the beginning of the clip. all seemed to make sense

looks like all the ones I thought batched successfully are behaving one way in the viewer (smoothly) and another in the timeline (freeze at every fourth) WHY?!!!? it just seems so arbitrary.