Sorry, roddlesnyc,
but this bug has nothing to do with smtp servers.
Me.com mail aliases (you can have up to 5 different aliases pointing to the same @me.com address) all use the same smtp server (and if you use iCloud this smtp server it's just called… iCloud, you don't even see the address).
Before Mountain Lion when I replied to a mail sent to alias1@me.com my reply was sent from "alias1@me.com"; when I replied to a mail sent to alias2@me.com my reply was sent from "alias2@me.com", and so on, even if my "alias1@me.com" mail was stored in a folder called "1" and my "alias2@me.com" mail in a folder called "2".
In Mountain Lion there is no problem if the mails are left in their own mailbox, but if they are moved to a different folder, the address that shows up in the "from" field is always the main one. This means that I've already sent a few mails from an address I didn't want to disclose (that's the point of having mail aliases, so that you can use an address for shopping, and another one for online forums, and so on, without revealing your main address).
Now I have to pay attention every time I send a reply, and manually change the "from" field to the correct one.