Steps to replicate:
1. Have 2 profiles.
Let's say profile A uses Minecraft version A and game directory A and profile B uses Minecraft version B and game directory B. I am assuming that you did select your client to close when Minecraft launches successfully.
2. Select profile A.
3. Click "Play".
4.Before Minecraft the game launches, change your profile selected to profile B.
5.Observe.

What I expected to happen was...:
The game was to use version A and game directory A.

What actually happened was...:
When your minecraft has launched, observe how it is of minecraft version A but is using game directory B.

Sidenote: As this involves the client not the game, I have been forced to select a version in affected version.
This is of the client version 1.3.1
I am uncertain if this has affected other version of client.