Haha, yeah that bug is still around. I reported it some years ago. Got good memories of testing this back in the day.
You can read it here: http://digiprose.com/phpBB3/viewtopic.php?f=6&t=8162
After the ship re-pressurizes you will not take damage anymore.
It is supposedly just the logic of the game, if you are in an atmosphere but taking damage from no life-support, the game assumes it is the atmosphere that is toxic.
As for the taking collision damage from recalling, that might be related to the new "fall damage" or something.
You can read it here: http://digiprose.com/phpBB3/viewtopic.php?f=6&t=8162
After the ship re-pressurizes you will not take damage anymore.
It is supposedly just the logic of the game, if you are in an atmosphere but taking damage from no life-support, the game assumes it is the atmosphere that is toxic.
As for the taking collision damage from recalling, that might be related to the new "fall damage" or something.