home_url() uses get_home_url() which in turn uses get_option( 'home' ) to retrieve the home url. The code in get_option() includes this:
// If home is not set use siteurl.
if ( 'home' == $option && '' == $value )
return get_option( 'siteurl' );
I didn’t unwind all the previous code in the function, but it seems likely that under some circumstances get_option( 'siteurl' ) does not match home_url(). Apparently, you found one of those circumstances. Try using site_url() in this case.
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