Comment 5 for bug 777882

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.