Simple to reproduce (for me anyway!)

Create a 9x9x9 cube (see http://i53.tinypic.com/zswpyf.png).

Use the wand to select the cube, so your selection region is then also 9x9x9.

//copy

//expand 30 30 e

//expand 30 30 s

//set #clipboard

You would expect the cube to be replicated correctly throughout the area, but torches are rotated and some parts are thinner than you'd expect.

See: http://i52.tinypic.com/1tllhc.png

Currently the pattern's origin is the world's origin (0, 0, 0) and so it is likely not pasting as you are intending. I will have to look into the torch issue though.

I understand why it wouldn't paste it back in exactly the same place (due to the different origin), however it pasted one part a different size (you can see in the screenshot that while every column should be two blocks square, one was only one block wide).

Meh... closed by mistake, sorry!

Make a ticket there I guess.