The key elements in the XF86Config file that affect what resolutions you have available and which one X defaults to are (1) the video card driver you are using (and possibly the setting for video memory, but this is not usually needed or used for modern video cards in XFree86 4.x), (2) the frequency ranges your monitor is set to use, and (3) the settings in your "Screen" Section, specifically the default color depth and the corresponding "Display" Subsection.
Apparently you now have the third element set correctly (i.e. the desired default depth and the appropriate Modes for it with the default resolution as the first Mode). It would seem likely that you have the correct video driver, although it is worth double checking. So the most likely problem would be that you don't have the correct frequency setting for your monitor. In the "Monitor" Section of your XF86Config file there are the settings HorizSync and VertRefresh. The values these should have vary according to the monitor you are using, so you will have to determine what the correct settings are based on the manufacturer specifications for your monitor model. If they are set incorrectly, then X will calculate the wrong set of possible resolutions available for your configuration.