OK...
If you havn't done so...turn DEBUGGING on.Site administration > Appearance > Themes > Theme settings It's the top box. Also set Designer Mode to ON as this stops Moodle from cacheing.
You could then try checking out theme/base/layout/general.php and theme/base/layout/frontpage.php to see if there is nothing strange about the php code. Also, check to see there are no white spaces left at the bottom of the config.php in the root directory?
The config.php has all the information needed for each page to access information from the database and also the $CFG->wwwroot without which it will get lost. So make sure all the information is correct.
You could also check to see all the theme folders/sub-folders are inplace? Theme config.php especially.
Have you made any alterations to ANY file in this new install? If you have, then the problem may be related to the type of Text Editor you used.
Have you uploaded any NEW themes to the theme folder? If so which?
The reason for me asking all these questions, is that the problem you have is caused by the fact the theme, any theme for that matter, it's not connecting to the CSS files it needs to display properly. The only CSS it's finding is from the YUI CSS files found in moodle/lib/yui/../../..
You might like to put this question "Theme not displaying after Moodle 2.0 install" on the THEMES forum. One of the Moodle Developers may be able to help you fix it.
Sorry I can't be more helpful...it's a real puzzle.
Mary