You need to convert the H264 files to ProRes.
I would suggest either LT or 422 for T3i footage. This is usually done via the log and transfer tool however you need to install the Canon plug in first. You can also use other apps like !Peg Streamclip for this. There is lots of info here about DSLR to FCP.
Golden rule though, don't edit H264 always convert to ProRes first.
best wishes
Neil
http://www.patience.tv