To reproduce, first reset all XKB options 
 
$ setxkbmap -option -option srvrkeys:none 
 
Now press control-shift-x and watch correct result in xev 
 
$ xev 
... 
KeyPress event, serial 30, synthetic NO, window 0x3400001, 
    root 0x72, subw 0x0, time 18906299, (54,126), root:(1269,151), 
    state 0x0, keycode 37 (keysym 0xffe3, Control_L), same_screen YES, 
    XLookupString gives 0 bytes: 
    XmbLookupString gives 0 bytes: 
    XFilterEvent returns: False 
 
KeyPress event, serial 30, synthetic NO, window 0x3400001, 
    root 0x72, subw 0x0, time 18906303, (54,126), root:(1269,151), 
    state 0x4, keycode 50 (keysym 0xffe1, Shift_L), same_screen YES, 
    XLookupString gives 0 bytes: 
    XmbLookupString gives 0 bytes: 
    XFilterEvent returns: False 
 
KeyPress event, serial 30, synthetic NO, window 0x3400001, 
    root 0x72, subw 0x0, time 18909298, (54,126), root:(1269,151), 
    state 0x5, keycode 53 (keysym 0x58, X), same_screen YES, 
    XLookupString gives 1 bytes: (18) "▒" 
    XmbLookupString gives 1 bytes: (18) "▒" 
    XFilterEvent returns: False 
 
Control-Shift-X is correctly reported as an event. Now swap control and 
caps-lock keys. 
 
$ setxkbmap -option -option srvrkeys:none,ctrl:swapcaps 
 
... and try the same excercise again: 
 
$ xev 
... 
KeyPress event, serial 30, synthetic NO, window 0x3400001, 
    root 0x72, subw 0x0, time 19055073, (66,94), root:(1279,119), 
    state 0x0, keycode 66 (keysym 0xffe3, Control_L), same_screen YES, 
    XLookupString gives 0 bytes: 
    XmbLookupString gives 0 bytes: 
    XFilterEvent returns: False 
 
KeyPress event, serial 30, synthetic NO, window 0x3400001, 
    root 0x72, subw 0x0, time 19056614, (66,94), root:(1279,119), 
    state 0x4, keycode 50 (keysym 0xffe1, Shift_L), same_screen YES, 
    XLookupString gives 0 bytes: 
    XmbLookupString gives 0 bytes: 
    XFilterEvent returns: False 
 
And that's it, pressing x in addition to control and shift does not generate an 
event. Interestingly, not all control-shift-keys get killed this way. E.g., for 
me, the effect occurs only for the key column containing x,s,w,2. 
 
My keyboard is an IBM Model M connected via PS/2 to a Dell Latitude C810 laptop 
running Gentoo Linux, kernel 2.4.27. XKB is set as follows: 
 
$ setxkbmap -print 
xkb_keymap { 
        xkb_keycodes  { include "xfree86+aliases(qwerty)"       }; 
        xkb_types     { include "complete"      }; 
        xkb_compat    { include "complete"      }; 
        xkb_symbols   { include 
"pc/pc(pc104)+pc/us+ctrl(swapcaps)+srvr_ctrl(no_srvr_keys)"     }; 
        xkb_geometry  { include "pc(pc104)"     }; 
}; 
 
Changing the keyboard type to pc101 and pc102 does not affect the misbehavior I 
observe.