Photoshopcs6  merge layers function moving images after merge

I'm trying to create a tiled texture using a seamless image. too bad its bricks. ive been having this issue throughout all of the photoshop steps in this experience. I'm pasting another image of the same before it in a new layer. merging it. created a line doing this. copied that line. merged it. fine.
copied new line. pasted. merged. BOOYAH! IM MOVING YOUR IMAGE AFTER MERGE!! BWAAHAHAHAHAHA IM EVIL!!!!.
why is this happening. I'm not doing anything different. This keeps happening. over and over again.
On my last file, I didnt even merge all the layers. I saved the file out as a png, and the result was the same as if I had merged the layers, which moves everything around. what do i need to change?!

Please post screenshots to illustrate the issue.

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