In Options Menu, Message sessions, Messaging tab, I have the 'Close the message window on send' box checked off.
As of the latest update received today (current version is .95.6 build 18429), the message window no longer closes after sending.
Minimize on send has no effect on the window after sending either.
This applies to a Jabber (Google talk) session. I don't have any other accounts running so can't confirm beyond that.
Edit: tried to install CrashDumper to provide better version info but I'm getting "An error occurred while checking for new updates" when I try to bring up Available Components List.
Edit edit: just saw move of development to github. Reporting this there.