Minor annoyance - I have my build/message windows docked to the bottom of the screen and set to auto-hide. If I double click on the line to bring it up in the editor to see it in context, 99.999995% of the time that section of code will be underneath the popped up window! (Maybe 99.9995%... I might be exaggerating...

).
The quirk seems to be that SE will open the file and "scroll down" to the line in question which will put it at the bottom of the screen - Which just so happens to be obscured by the pop-up...
It'd be nice if SE could be smart about this and adjust the text position accordingly (especially with all windows being "full screen" now... I didn't have this problem as much with the old MDI layout (cough, cough) )