So, I have a keyboard with a backlight function (at night it's very annoying when I have to turn on the light just to se what I'm typing). The backlight is controled by the scroll lock led: when the led is on, the backlight is too and oposite. I spent a few hours the other day figuring out how to turn on the scroll lock led, because pushing the Scroll Lock key in Xorg (by default) doesn't do anything. I knew that xset led 3 would work, so I try'ed to setup xbindkeys so that a shell script would be executed whenever I pressed the Scroll Lock key. It worked, the script was getting executed, but I didn't know how to setup the script so that it turned the led on when it is off and off when it's on. So I gave up on xbindkeys, and found xmodmap. Then after a hour or so i figured out that I could set mod3 (a modifier key witch was empty) to Scroll_Lock and everithing worked. I was happy. Well sort of: by that time I also discovered that the keyboard ain't worth shit.

Everything was ok after that, till today. I turned Scroll Lock on, and then tryed to switch windows with Alt+Tab. Nothing happend. Then I tryed Pressing Alt+F in firefox (to check if the Alt key is disabled all together) and it opend the File menu just like it is suposed to. My conclusion is that any spetial action of the modifier keys is disabled when Scroll Lock is enabled, but other actions work (WTF am I even saying). The Win key doesn't work properly either. I use those keys all the time so this type of behaviour isn't acceptable.

Can I make the keys unrelated to Scroll Lock? When I turn the scroll lock led on via xset, all the keys work normally. So the Scroll Lock functionality is not set in that case.

PS: I'm on Gnome if it makes a difference.

Note: I have asked the same question over at arch linux forum, but nobody replied.

Would you post your configurations and scripts that you use to do this? The ones that you have edited, so we might be able to diagnose the problem...

All I did was:
xmodmap -e "add mod3 = Scroll_Lock"
That enables the standard use of the Scroll Lock key on a keyboard. Then if I activate scroll lock in X, the standard functionality doesn't work anymore. For example, I can't do Alt+Tab to switch windows, nor can I use the Win key to controll my music player. But, on the other hand, Alt works for menues. If I press Alt+F in firefox, it opens the menu as normal.