configuration files not respected on ubuntu?

I have recently installed ion3 and am trying to use the windows key 
rather than the alt key for META.  xmodmap shows the windows key is 
Mod4, so I made the following edit to cfg_ion.lua in my ~/.ion3/ directory:

-- Set default modifiers. Alt should usually be mapped to Mod1 on
-- XFree86-based systems. The flying window keys are probably Mod3
-- or Mod4; see the output of 'xmodmap'.
META="Mod4+"
--ALTMETA=""

from

-- Set default modifiers. Alt should usually be mapped to Mod1 on
-- XFree86-based systems. The flying window keys are probably Mod3
-- or Mod4; see the output of 'xmodmap'.
-- META="Mod1+"
--ALTMETA=""

I restarted the session and nothing doing.  I restarted my computer and 
still windows does nothing.

I then made a different edit which had no effect.  I commented line 237 
in ~/.ion3/cfg_ioncore.lua  so that Meta-P's default behavior is 
disabled.  I again restarted my computer and witnessed no effect.

What am I doing wrong?

I might also take this time to ask what the best way is to test 
configuration changes.  I have been logging in and out.  Is there a 
better/faster way?

Thanks,
Red

p.s.  I am running the ion3 that I apt-got with my ubuntu feisty machine.
> $ ion3 -V
> 3ds-20061029