Steps to reproduce:

- Use the attached .B25.blend as the default configuration file (ie. copy the file into $home/.blender/ or whatever place it should be in)
- Start Blender
- Use Alt + Left Mouse to rotate the 3d view: this works
- Use Left Mouse to drag a border: works as well
- Now press Alt + Tab to switch to another window (I've only tested other OS windows, not Blender windows)
- Use Alt + Tab again to switch back into the Blender window
- Try to use Alt + Left Mouse to rotate the 3d view again

It will now do border selection (ie. what's assigned to the Left Mouse shortcut, without key modifiers) instead of rotating the view ("view3d.rotate" is assigned to Alt + Left Mouse in the attached .B25.blend).

Only after clicking with the Left Mouse button again, it will return to the assigned behavior from the key configuration.

Normally, this bug will go unnoticed because the default Blender keymap configuration doesn't have such shortcuts (as far as I know), it will only show up with settings as in the attached file. These settings make Blender's behavior a little more like programs such as Silo or Maya.

For me, the bug shows up when using Blender 2.5 (latest svn) on Windows (Vista, SP1). I don't know if it happens on Linux and/or OSX as well.