What size is the Mpeg2 format? What Pixel Aspect Ratio? After Effects always handles different sizes and pixel aspect ratios correctly if you have not mucked up the settings somewhere in the chain.
Please show us info on your footage that includes frame size, frame rate, and compression. Then Please show us the information on your compositions.
I use a canon legria fs306 camera. My site is www.wexfordads.ie . I have AE CS6. I have to convert the imported videos to other formats to avoid the cropping.
You still didn't tell us anything at all about your video footage. Don't know the frame size or the pixel aspect ratio. We also have no idea what you are trying to output. Sorry I can't be of more help.