emacs22 black text on white bg from menu but white text on black bg from console

[Micha Feigin <michf@post.tau.ac.il>]

I have a strange setup issue.

I removed my emacs settings to redo them so now there are no theme commands
(clean .emacs). Now, when I open emacs from the menus or file manager (thunar)
it comes up in a dark text on light background theme (not very readable with
the match of fonts and colors), and when I open it from rxvt (or any other
console) it comes up in light text on dark background (much better for my
taste).

What is the difference, and how do I make one of them my default instead of
getting different behaviour?

Thanks