Problem with the scale of pictures when importing.

I have taken 250 images which I will edit into a stop motion film. however, I've encountered a few problems.
The biggest problem is that when I imported the images into the timeline they were severely magnified and not even centered in the frame. as you can see by this screenshot:
This is a big problem. You'd think I wouldn't have to go through every signle image and scale it down to correctly fit the frame..... right?? It's not even centered which means I have to scale and move and be very accurate and it's going to take so many hours to do! What is wrong here, how do I fix it so that when I import the images, they are the correct scale?
problem 2: when i put the images in the timeline they were "backwards". As in, the last image was first in the timeline and the first image was last. It's like the program is TRYING to make my life a living hell.

I upgraded to cs6 and imported all the images together, I made them 3 frames per and exported them. The problem is slightly improved but still there. I'm still getting flicker.
Check it out: http://www.youtube.com/watch?v=g_yZjskzTLs
Black screen version from yesterday if you want to look at it: http://www.youtube.com/watch?v=NCcAEO8YU6Y
The problem has to be with my settings. when I upgraded it deleted all my prefrences and settings. There was no dslr preset either so I had to redo it all from scratch to the best of my ability. Here is a complete rundown of my settings:
I shoot with a canon dslr 60D in 24fps and upload all my stuff in 1080p. Please advice.

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