found a solution to my problem:

Instead of doing:
  remove Lock = Caps_Lock
  add mod5 = Caps_Lock

I had to do:
  remove Lock = Caps_Lock 
  remove mod5 =  ISO_Level3_Shift
  keysym Caps_Lock = ISO_Level3_Shift
  add mod5 = ISO_Level3_Shift

The resulting "xmodmap -pm" looks like this (0x42 is caps_lock):

xmodmap:  up to 4 keys per modifier, (keycodes in parentheses):

shift       Shift_L (0x32),  Shift_R (0x3e)
lock      
control     Control_L (0x25),  Control_R (0x69)
mod1        Alt_L (0x40),  Alt_R (0x6c),  Meta_L (0xcd)
mod2        Num_Lock (0x4d)
mod3      
mod4        Super_L (0x85),  Super_R (0x86),  Super_L (0xce),  Hyper_L (0xcf)
mod5        ISO_Level3_Shift (0x42),  ISO_Level3_Shift (0x5c),  Mode_switch 
(0xcb)


Hopefully this will help in tracking down the bug.

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https://bugs.launchpad.net/bugs/777882

Title:
  xmodmap not honored

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