Description:
Some key events that I want are being captured before I get them. This started several months ago (summer 2011?) but was momentarily fixed a few days ago. It's broken again today (I did a normal upgrade including to linux-3.2.5).

Some of the keys are completely gone (e.g. C-M-a; with my remapping described below, this means both left and right keys marked "alt") in the sense that they deliver no events to Xmonad or xev. Holding the left keys marked "control" and "alt" instead (even though xmodmap should make these two chording variants equivalent) works as desired.

Other keys are still generating events, but not one that is useful. The following xev output comes from holding Super_L (mapped as key with windows logo), pressing "l", and releasing Super_L.

KeyPress event, serial 30, synthetic NO, window 0x3c00001,
root 0xac, subw 0x0, time 7298944, (1125,563), root:(1127,565),
state 0x0, keycode 133 (keysym 0xffeb, Super_L), same_screen YES,
XLookupString gives 0 bytes:
XmbLookupString gives 0 bytes:
XFilterEvent returns: False

FocusOut event, serial 30, synthetic NO, window 0x3c00001,
mode NotifyGrab, detail NotifyAncestor

FocusIn event, serial 30, synthetic NO, window 0x3c00001,
mode NotifyUngrab, detail NotifyAncestor

KeymapNotify event, serial 30, synthetic NO, window 0x0,
keys: 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

KeyRelease event, serial 30, synthetic NO, window 0x3c00001,
root 0xac, subw 0x0, time 7301856, (1125,563), root:(1127,565),
state 0x40, keycode 133 (keysym 0xffeb, Super_L), same_screen YES,
XLookupString gives 0 bytes:
XFilterEvent returns: False

Contrast to exactly the same process with "x" instead of "l":

KeyPress event, serial 30, synthetic NO, window 0x3c00001,
root 0xac, subw 0x0, time 7514809, (874,518), root:(876,520),
state 0x0, keycode 133 (keysym 0xffeb, Super_L), same_screen YES,
XLookupString gives 0 bytes:
XmbLookupString gives 0 bytes:
XFilterEvent returns: False

KeyPress event, serial 30, synthetic NO, window 0x3c00001,
root 0xac, subw 0x0, time 7516277, (874,518), root:(876,520),
state 0x40, keycode 56 (keysym 0x78, x), same_screen YES,
XLookupString gives 1 bytes: (78) "x"
XmbLookupString gives 1 bytes: (78) "x"
XFilterEvent returns: False

KeyRelease event, serial 30, synthetic NO, window 0x3c00001,
root 0xac, subw 0x0, time 7516393, (874,518), root:(876,520),
state 0x40, keycode 56 (keysym 0x78, x), same_screen YES,
XLookupString gives 1 bytes: (78) "x"
XFilterEvent returns: False

KeyRelease event, serial 30, synthetic NO, window 0x3c00001,
root 0xac, subw 0x0, time 7516760, (874,518), root:(876,520),
state 0x40, keycode 133 (keysym 0xffeb, Super_L), same_screen YES,
XLookupString gives 0 bytes:
XFilterEvent returns: False


Additional info:
I normally use a somewhat unique configuration, xmonad as window manager with gnome session, dvorak layout, right Alt key mapped to Control_R. My computer is an Asus U46E.

Steps to reproduce:
These key combinations never work. I tried a couple months ago with stripped down/standard settings, but these key events still did not work. It was also appeared with a different computer, but not for all the same keys. I haven't tested that machine recently.

I'm reporting this because it started working a few days ago and then broke again (after upgrading from linux-3.2.4 to 3.2.5, but I updated other packages at the same time and tried haven't bisecting group of packages).