One of the things you could try is to make all the layers invisible except the two you want to merge, then tell it "Merge All Visible". sometimes that will overcome the issue you're describing.. I've had weird merging effects myself. The quick way to do that if you don't know already, hold Alt when you click on the little eye to make all the other layers invisible, then make the second one visible again (i think that's how you do it if i remember correctly)