YOu've got a visibly dirty piece of metal...what is happening is whatever the substance is on the top, is being "scratched" deeper into the metal. No amount of etching can rid the metal of that kind of contamination. When welded it can definitely cause issues. Another thing you have to consider, since aluminum doesn't rust, but does oxidize, is how deep the oxidation goes. With the amount of visible staining on top here, and any interaction with steel and a cathode/anode interaction, (if this is the case) you will have extra deep oxidation. Ever try to weld on an aluminum boat that's been in salt water? Not the easiest thing in the world.