I am going to reiterate much of what has been posted here and also include my configuration and the error/bug I have been experiencing. I am repeating things so that we can be sure that we're all on the same page as well as to explain to those who may potential help as to the issues that we;re experiencing.
I have a total of eleven (11) e-mail addresses, which include my iCloud account. The majority of the addresses are POP3. I have that many addresses because of my business and each e-mail is for a specific web site. In order to sync my e-mails across the multiple computers I have, I created a rule that would move every e-mail I received to the iCloud account.
In Lion, even though the e-mail was moved to the iCloud account, when I replied to an e-mail, it would reply from the account to which the e-mail was sent. Thus, if an e-mail was sent to 'tony@mydomain.com', it would be moved to the iCloud account (which would sync it among all computers). Replying to it would be sent from 'tony@mydomain.com' and use that server and its settings.
This has been broken by Mountain Lion and Mail 6.0. Now, an e-mail is received and moved to iCloud. But, when replying, the reply-from address is now the iCloud address -- NOT the e-mail address to which the e-mail was sent.
This STILL works in Lion. I have a machine running Lion and have been using it side-by-side with MountainLion.
Now, a couple of things I have discovered.
While entering e-mail aliases into the e-mail address of the iCloud settings seems to work, it actually causes a couple of problems. First, it causes the iCloud syncing to not work -- the "Mail" box becomes unchecked in System Preferences for iCloud and won't stay checked so long as the "foreign" (non-iCloud) e-mail address is in the account settings for iCloud.
Second, the server settings for the outgoing e-mail get broken. It's weird. E-mails don't send at times.
I sincerely hope that Apple fixes this. People may suggest that I use IMAP accounts to sync my e-mails. That is not an option. The web host I use only allows a certain number of processes to run. With all my e-mail accounts, checking my e-mail would easily blow me past that number.
Well, that's the situation. If someone can shed some light with their expertise, it would be greatly appreciated. I will also be filing a bug report with Apple. I hope that they cane fix this in the .1 release.
All the BEST!
T.