I was bitten by the same bug while using a specific ~/.xmodmaprc to switch the 
option and command keys
on a macintosh keyboard.

Applying the following patch works around the problem:

 ! Remove Mod1 and Mod4 mappings (as shown by xmodmap on fresh config)
-remove Mod1 = Alt_L
-remove Mod1 = Meta_L
+clear Mod1
+clear Mod4
 
-remove Mod4 = Super_L
-remove Mod4 = Hyper_L
+! clear some mess coming out from ?
+keycode 204 = NoSymbol NoSymbol NoSymbol NoSymbol
+keycode 205 = NoSymbol NoSymbol NoSymbol NoSymbol
+keycode 206 = NoSymbol NoSymbol NoSymbol NoSymbol
+keycode 207 = NoSymbol NoSymbol NoSymbol NoSymbol
 
 ! Add keycodes as shown by xev
-keycode 64 = Super_L
-keycode 108 = Super_R
-keycode 133 = Alt_L
-keycode 134 = Alt_R
+keycode 64 = Super_L Super_L Super_L Super_L
+keycode 108 = Super_R Super_R Super_R Super_R
+keycode 133 = Alt_L Alt_L Alt_L Alt_L
+keycode 134 = Alt_R Alt_R Alt_R Alt_R

I have tracked down precisely which of the modifications (clearing the 205-207 
keycodes, using 'clear'
 instead of 'remove' to clean the modifiers or settings the four values for the 
keycodes) addressed the problem.

Hopefully the xorg-server hackers may under the issue better than me.

-- 
xmodmap failure BadValue error, 118 (X_SetModifierMapping)
https://bugs.launchpad.net/bugs/524774
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