Timings off on 59.98fps Conformed Footage

This is the first time I'm really using Color to it's fullest potential, so a quick disclaimer that it could be something obvious. Anyhoo, here's the deal: I'm editing some stuff I shot on the Sony FS100. Most of the footage I shot was 1080p 23.98 fps, but there were a few sequences I wanted at 1080p 59.98fps to get the slow motion effect. I'm done editing and have exported to Color, but the sequences that were shot in 59.98fps and conformed to 23.98fps are not showing up properly in Color. Everything plays fine in FCP 7, but when I export to Color, it shows the clip duration from the beginning of the clip rather than the proper in/out points. I've posted the workflow below, so any help would be much appreciated.

FS100 1080p 60fps Workflow:
1. Transcode AVCHD files to ProRes HQ in ClipWrap without altering framerate (conforming to other framerates is now an option in ClipWrap, but they only have an option for 24fps, not 23.98, so I didn't want to risk it).
2. For 59.98fps footage, do an additional transcode (ProRes HQ) with MPEGStreamclip because Cinema Tools won't conform the footage straight out of ClipWrap.
3. Do a batch conform of the 59.98fps footage to 23.98 in Cinema Tools.
4. Import everything into FCP 7 and edit.
5. Export to Color. Everything looks good except for the timing of the conformed footage.

Thoughts?

Thanks!