Left Shift and Left Command combination yields only Left Command; other shift command combos work fine Early 2011 15" Macbook Pro, Lion, no external keyboard or mouse:

Lately I noticed that I can't use left-shift+left-command together; it registers as left-command only.  The other three combinations (right-shift+right-command, right-shift+left-command, left-shift+right-command) work properly. I’ve confirmed this in text editors and in the keyboard viewer.

Same problem appears with left-command+left-control.

I’ve shut down all programs, verified no weird keybinds in Universal Access or elsewhere, even installed Lion to a clean external disk and booted from that.  The first thing I did was check left-shift and left-command in TextEdit; same problem.

Any ideas?
I'm posting the non-answer of "I reinstalled OSX and upgraded to Maverick from Lion, and it now works" because, well, it now works. Unfortunately I don't know what were the actual reasons it broken and then un-broken. I am sorry to anyone whom this question didn't help at all.

If anyone else comes up with a reasonable explanation I'll mark them as the answer instead.