This discussion is getting sidetracked by rules, and reply-to's. Try this simple test:
COMPOSE a new message. You need to have 3 accounts in mail for this test. The one that's constantly showing up as the reply-to address? Leave it out of the correspondence. Send a message from one account to the other.
Does the third account still show up as the reply-to? Okay, that's the problem.
Of your three accounts, are two of them gmail accounts? Yes...
Verify in Mail Preferences that the proper SMPT server is selected for each of the accounts. They are both identified in the drop-down only as GMAIL, so make sure you don't have the first one checked for both accounts, or the second one checked for both accounts.
Setting this straight solved this for me, and stopped my business account from being the default reply-to no matter what inbox was selected at the time. And personal replies cluttering my business inbox (ugh!)
This is not an Apple bug. It is a problem of creating a feedback loop through the two gmail accounts. Everything works properly when you set it up properly.