I've two accounts, let's call them A (internally 1) and B (internally 2). A is default, A is current account, I'm in the "Inbox" folder belonging to A, I've selected a message addressed to A. However, when I hit "Reply", "Forward" or "Compose", account B is selected as "From" in the new message, and B's signature is appended. Same happens if I'm in "Sent" or "Trash" of A: "From" of any new, reply or forward message is B. If I'm in some other folder of A, and reply, forward or compose, "From" is correctly set to A. "Automatic account selection" is all on.
Are your 2 accounts both IMAP accounts?
A is POP3, B is IMAP. Both have their own, separate SMTP for outgoing mails.
First point is that a POP account has no direct connection to an MH mailbox, so the MH mailbox is not account A's mailbox, it just makes use of it. If you had a 2nd POP account it too could use that mailbox. Automatic account selection is based primarily on recipient headers and not mailboxes. As automatic account selection has worked fine for me for many years, I am inclined to think that it also does for you but there is an assumption that it should somehow work differently. However, with the use of 'A' and 'B' and no mention of actual values of your account email addresses or those in the headers of the messages in question it's not possible to explain further. One last point, which may be pertinent: you can set default accounts for the various actions in the folder properties.
Your remarks solved the problem. Definitely not a problem of account selection (works as defined), but perhaps a problem of initial folder or account creation: For all the "predefined" folders in the MH Mailbox (Inbox, Sent, Drafts, Trash, Queue), the default account was explicitely set to B (I don't know why, I'm quite sure I did not do this). Corrected that, problem gone...