If you are at the update screen in minecraft and click a Windows related screen with the same options Yes / no. Minecraft will perform actions.
Example.
1. Load up minecraft to "Do you want to update?"
2. Load bandi cam / Fraps
3. Windoes 7 + will ask if you want the program to run.
4. Click yes you want on the windows 7 screen to load your video recorder
5. Minecraft updates while still showing the "Do you want to update?" screen w/o you clicking yes in minecraft.
EDIT
This affects ALL versions of minecraft including Current versions!
This is not a click through the yes/no screen can be anywhere on your screen and still affect minecraft
Comments 4
This is probably a click through from the window on top of minecraft. Can you move the yes/no prompt window and then click in it and see if it still does what you are saying?
Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
Please, don't mark bugs as "Affecting future (unreleased) versions".