I can't figure it out from your description, but I'll (1) ask you some probing questions; (2) give you some paths to go down, in case you haven't already:
* does the keyboard work in the `plain' console (the one you get to by hitting C-M-F[1-6]?
* does loadkeys work?
* does xev produce correct output? (have it run in a terminal, then hit a few keys)
* does gkb_xmmap and/or setxkbmap work?
* go to (control-panel-like-thing) -> ... -> keyboard; does your `physical' keyboard model match your `logical' model?
* (same place) is the layout sensible?
* does .Xdefaults look sensible?
* try this:
$ echo | xrdb -load -
** in case that produces a new look that you don't like, use this as a template for restoring your settings:
xterm*Border: dark blue
xterm*ttyModes: intr ^c susp ^@ dsusp ^@ kill ^u eof ^d
if all else fails: Don't panic
hope this helps,