xemacs and key mapping problems

For some time now I have got a warning when starting xemacs. The warning causes the window to be split into two, with the warning in the lower window. The warning is something to do with the keyboard mapping having mod1 and mod3 defined to the same key. I googled for answers but they all said the same - fix it using xmodmap. I tried it and it didn't work. So in the end I added the following to the end of my .emacs startup file:

(when (featurep 'xemacs) 
;; Don't warn me about nonsensical X11 modifier issues. I don't care 
;; if Alt is simultaneously Mod2 and Mod5 on this machine; I don't 
;; press it anyway. Yay separate Meta keys. :) 
(setq display-warning-minimum-level 'error) 
(setq log-warning-minimal-level 'info))