Ok I try explain. You have accounts on your server for example user1@domain.com and user2@domain.com
1. User2 can reply to user1 ? You will see replies ?
2. When you receive mail from gmail (or another external mail server ) and later you write reply - gmail account receive your reply ?
3. When gmail account recieve your mail from user1 (for example) and write reply - user1 receive reply from gmail ?
4. When user1,user2 and gmail account write reply - what address you can see in address string - its correct reply address ?
5. This problem only with replies and another message (incomming, outgoing) work fine to/from your domain.com and external mail servers ?
6. I mean imap and smtp server log for check what's going on, may be some problem with replies addresses or similar.
So we need check its problem only with replies and what back address for replies used.
You can open your sender mail and click on HEADER link to see what replies address you have in string FROM (like on screenshot) - its correct ?