When stabalizing, After Effects can’t “create” the missing pixels. Instead, it moves the whole clip around, so that the point you stabalized stays in one place. One way to fix this is to scale the clip just a little bigger so it fills the frame. Another way is to repeat the edge pixels. I saw this in a tutorial by Andrew Cramer. In version 6.5, the plug is under the ‘stylize’ menu, it’s called ‘motion tile.’ By setting the output width and output height to the amount of pixels you’re missing on the edge, and checking the ‘mirror edges’ checkbox, it’s going to repeat the outermost pixels of the image. Beware though, it doesn’t work in all instances.
Hope that helped,
-A.N.