[WNC Goater]

Melting it shouldn't change the properties of the brass, as long as it wasn't grossly overheated perhaps burning out some alloy, though I think that is unlikely.

In my years of polishing metals, it is very important to take it as far as you can with finer and finer abrasives before actually starting to buff. Otherwise, it is difficult to notice some deeper scratches, until you've already spent time buffing, and then those deeper scratches become more apparent.
So make sure you are getting "to the bottom of things" with previous scratches, before moving on to finer polishing compounds.
Now you indicate you have done that and at the finest grits scratches are showing up. So some possible causes:

Are you using a buffing wheel dedicated to a particular grit of compound? Meaning, you aren't using the same buff for finer compounds that you previously used for heavier grit compounds?

Is the buff clean? If you use one buff for steel and the same buff for brass, there could be minute steel residue clinging to the buff that is cutting into the brass. Ideally, you would have buffs that are dedicated to the individual compound and the individual metal.

Do you have a buff rake or some type of tool to clean the buff?

Also be aware you could potentially cause cross-contamination from the face of your buffing compound. Steel can get deposited on there and transferred to the buff used for brass.

There is no possibility of contamination from grit released from a grinding belt? There is no residual grinding dust on the brass as you start buffing?

Just a few things that come to mind. I doubt what you are experiencing is a result of some abnomality caused by melting the brass.

One final thought. Satin finish with scotchbrite rather than bright polished guard. Some metals are just difficult to get a mirror polish on. Just a thought...