A sent email should not affect the order of a conversation in your inbox
Currently, when you respond to an email with conversation mode enabled, the conversation then appears at the top of your inbox. I don't think any other email client with conversation sorting handles it this way. A response should not move that email to the top of your inbox. It should remain in chronological order based on the last email you received.
Beta version 2.0 was released and it has this bug fixed.
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Boxer inbox just set run but don't bring up the emails
Awesome, thank you for the quick response.