I shot a clip with a JVC HD100, in HD-SD60P. I streamclip a quicktime movie, open it in cinema tools. But the conform box is greyed out where i cannot select it. Why is this? Ive brought quicktime movies into CT and conformed many times. Does it need to be downconverted, or a particular codec? What gives?

If you mean for slow motion, what I've done after capturing in DVHScap, I convert to AIC in MPEGStreamclip. I forget the exact settings (when I messed them up, I just got a green clip for the output), but you in general, you want progressive and leave the resolution pretty much alone. After I did that, opening in Cinema Tools was no problem.

I'm sure other codecs are fine - are you sticking with HDV? You might need to go to a non-long GOP format, like AIC, DVcpro HD, or uncompressed.