rajupp - snide remarks don't encourage help from support people either. Please be polite.
I don't know why that happens. Please list your plugins, your theme (and url to theme) and what's on your front page (posts or a static page).
When you get the 404, is it a WordPress 404 page or is it a generic Apache 404? Do you have any plugin that does special things to catch 404 requests? Does the 404 request get cached in the wp-content/cache/supercache/hostname/index.html(.gz)?
Is the 404 recorded in a cached file in wp-content/cache/ ?
Does your theme or any of the plugins you have use query_posts()? That overwrites the 404 error flag and messes up the caching. There's already a fix in the plugin for that but there might other ways of overwriting the 404 status. The 404 page shouldn't be cached at all.