I created a launcher profile called "Time Machine" to use 1.5.2. This profile had the launcher set to keep open. I also made a folder called "Time Machine" to run the game in.
I then launched the game in that directory, and created a world called "Test".
When I relaunched the game, instead of using the custom folder, it used the main .minecraft folder, and did not have the world "Test".

It seems that this is fairly sporadic, but it's possible to manipulate it slightly. If you launch the game as soon as the launcher has loaded, it seems to launch in the correct directory 90% of the time. However, after that, it's totally random if it launches in the main directory or the user allocated directory.

The setting of the launcher's opening makes no difference, be it keep open or reopen after game close.

I have attached my log of 4 runs of the game with the launcher kept open, two launched into the correct directory and two launched into .minecraft. No options were changed, only the play button was clicked.