From time to time, with no warning, the game window will lose focus and minecraft will state that it is not responding. However, the map is still loaded, basically leaving the player immobile but still active as an entity on the server.
It occasionally occurs when switching focus to another window (the aforementioned unresponsiveness), but it is not consistent, and as mentioned before, it can happen whilst actively playing; the window loses focus, and becomes unresponsive. In neither case does the game pause, as if Esc was pressed to go to the menu. It also does not remember a previous key press, e.g. if the player is moving when the defocus occurs, they will stop moving.
This occurs in both single and multiplayer, and renders the game unplayable. The only solution to the defocus is to close the window, logging out of the server. This re-opens the launcher, stating that the game exited with an error code, yet does not write a crashlog to the .minecraft directory. The player is still an entity on the server; there is no logout message, and a non-LAN opened singleplayer world does not pause when the defocus occurs.
Closing the window to log out gives a disconnect.genericReason error in the server log (see attached). I have tested this using a local, singleplayer server, a multiplayer server hosted on the same computer, and also several multiplayer servers hosted externally.
After a period of time, which does not seem to be consistent (sometimes a few seconds, sometimes minutes), the game becomes responsive again, and can be used again.
I have not found any bugs which duplicate this on the bug reporter, On a slightly separate note I have found that I have a greatly reduced framerate in the affected versions of the game; I do not believe the two to be related, but it is a possibility. Also, the java.io.FileInputStream.readBytes error at the start of the server log has been occurring in all server versions since 1.6.1 on my computer, if they are launched with more RAM than is allocated by default, however this does not seem to have had any effect whatsoever on performance, responsiveness, etc.
I hope this report can be of use, thank you for your time.