I am also having a problem with Mail not sending emails from the correct account. I have two gmail accounts that I use in Mail, and one work account. I have different signatures in each. When I reply to a message I am sure to check which email account I am writing from, and it is obvious from my signature.
HOWEVER, when someone replies to my message it comes back to the wrong address, and when I look it appears that they received it from the wrong address as well. This happens when I send an email from my personal gmail account, and it comes back to me in my work account. I do not want people seeing my work account email, nor do I want personal emails in my work account. However, no matter how careful I am about checking which account I am in and writing from, this continues to happen.
This happens on my iPhone too. I get an email in my personal account, hit reply, and then when I get a response it goes to my work address, like that's where I sent it from. But I didn't, I just hit reply in the email - shouldn't it go from that account?????????
I have reported this to Apple, does it sound like the same problem you are all having?