So the portion you are trying to polish on your door...it's a replacement section? Right?
If so, it's probably a different alloy of aluminum as others have mentioned. We have a small patch on our street side that is a different aluminum composition...it'll never polish the same as the original panels. You can
buy the "right" aluminum when doing repairs, but a lot of people don't
because it is not as readily available. It may look okay when new...but it oxidizes differently and discolors over time.
It's a chemical composition thing...like comparing 12kt gold to 18kt gold...yes, they both are considered "gold", but the actual composition is 12 parts or 18 parts real gold (of 24 total parts) and the remaining is "some other metal". So 12kt has 50% gold and 50% something else and 18kt has 75% gold and 25% something else. They look and polish differently because the "something else" effects it.
Have you started polishing the other replacement sections? Do you know if all the replacements were done at the same time with the same materials? Are you having as much trouble with them?