It sounds like you’re perhaps importing the original clips off the card, instead of the combined clips generated by the C100 utility?
At any rate, I usually just copy the MTS files off the card (I think they are MTS….) and use them directly as opposed to using the utility, and assemble them together in their own sequence to get one complete clip to use in the larger project. I archive my projects to optical disc, and having smaller segments to write to disc makes life a little easier for me.
One thing to note on a different topic — I’ve run into issues with Premiere getting confused with long clips from the C100, where it doesn’t update the timeline when you play the sequence, and eventually just puts a red screen up in the preview window. I’ve had to convert the footage to the Cineform codec to get around this.
You also need to force Premiere to interpret 30P footage from a C100 as 30P — by default it sees it as 60i, and you get interlacing artifacts. (in case you’ve not run into this yet…)