You have created the problem by moving all of the menu css into the main.css file.
There are three files created by Menu writer.
menu.css - contains CSS For standards compliant browsers such as Fire Fox and Safari.
menu_ie.css - contains CSS for IE6 and under.
you have removed the menu.js file, removed the conditional comment that attaches the menu_ie.css file to IE6 and under and moved the css from both menu.css and menu_ie.css files to the main.css file.
by doing this, the css from the menu_ie.css is being used by all browsers, and so is the menu.css, this will cause conflicts in the css styles being applied.