According to the file xkb/symbols/jp, JP K/Bs(jp106/jp109) has 2 meanings
on the Caps Lock key, which are "Eisu_toggle" and "Caps_Lock":
    (snip)
    key <CAPS> { [ Eisu_toggle, Caps_Lock ]     };
    (snip)

If the option "ctrl:nocaps" is set at the same time, following settings
(from xkb/symbols/ctrl) are loaded:
    xkb_symbols "nocaps" {
      key <CAPS>  {  symbols[Group1]= [ Control_L ] };
      modifier_map  Control { <CAPS>, <LCTL> };
    };

So, the use of "ctrl:nocaps" for jp K/Bs result in
    key <CAPS> { [ Control_L, Caps_Lock ]     };

It means that Caps Lock+Shift doesn't work as Ctrl_L+Shift.
Unfortunately, if Caps Lock+Shift is pressed, it results Ctlr+Shift+Caps.

Actual Results(from the result of xev command):
  (snip)
  KeyPress event, serial 30, synthetic NO, window 0x3c00001,
     root 0x48, subw 0x0, time 1262610, (108,-58), root:(112,454),
     state 0x7, keycode 38 (keysym 0x61, a), same_screen YES,
  (snip)

Expected Results:
  (snip)
  KeyPress event, serial 32, synthetic NO, window 0x2400001,
    root 0x48, subw 0x0, time 14782148, (15,96), root:(607,272),
    state 0x5, keycode 38 (keysym 0x41, A), same_screen YES,
  (snip)

The expected results above obtained with modifying it as following:

--- /etc/X11/xkb/symbols/ctrl.orig      2004-09-29 04:20:47.000000000 +1000
+++ /etc/X11/xkb/symbols/ctrl   2005-05-01 20:56:39.824039696 +1000
@@ -3,7 +3,7 @@
 // eliminate the caps lock key completely (replace with control)
 partial modifier_keys
 xkb_symbols "nocaps" {
-    key <CAPS> {  symbols[Group1]= [ Control_L ] };
+    key <CAPS> {  symbols[Group1]= [ Control_L, Control_L ] };
     modifier_map  Control { <CAPS>, <LCTL> };
 };

Though I'm not sure how to fix it in the best way, my quick hack
works fine.