I've done some further testing, and checked log files, and it seems that after enabling 'Enable DMARC policy compliance check', the messages are timing out on receipt:
[2016.11.21] 14:05:18 [163.172.22.222][58517643] cmd: DATA
[2016.11.21] 14:05:18 [163.172.22.222][58517643] rsp: 354 Start mail input; end with <CRLF>.<CRLF>
[2016.11.21] 14:07:21 [163.172.22.222][58517643] rsp: 421 Command timeout, closing transmission channel
[2016.11.21] 14:07:21 [163.172.22.222][58517643] disconnected at 21/11/2016 2:07:21 PM
[2016.11.21] 14:07:27 [163.172.22.222][58517643] rsp: 250 OK
[2016.11.21] 14:07:27 [163.172.22.222][58517643] Data transfer succeeded, writing mail to 661855637653.eml
The sending server obviously doesn't think it's been delivered, and tries again approximately 30 minutes later. SmarterMail on the other hand is delivering the message to my inbox.
I've changed the SMTPin Timeout from 120 to 180 seconds and will see if that makes any difference.