Hi Eric
What kind of file did you send to the Cinec program?
I have found that ffmpeg (the backend that Cinec uses, as far as i know) has a different way to read YUV formats than Adobe apps, and when converting to a Prores i find it more reliable to send a RGB encoded file (eg. Quicktime None) to get around the way ffmpeg reads an 4:2:2 YUV file (eg. QT DNxHD or QT uncomressed YUV 10bit)