I recently had some issue's with footage out of the C100 which wasn't happy in Premiere Pro. To save me going through it all again, here is a link to my blog explaining...

Canon C100 Stress! | Digiflicks - Video & Photography by Simon BakerDigiflicks - Video & Photography by Simon Baker (http://digiflicks.co.nz/blog/canon-c100-stress/)

If anyone has had a similar issue I would love to hear about it and possibly get an answer etc

Cheers

UPDATED:

Premiere Pro is the problem..! As this camera is the first I have had that shoots AVCHD, I wasn't aware of the issue's it can cause. I am now transcoding using 5DtoRGB and all is fine....