I have in my site.ini:
[SiteSettings]
DefaultAccess=en

[SiteAccessSettings]
RemoveSiteAccessIfDefaultAccess=enabled

As a result, as expected, the siteAccess is not included in the url when I surf on the default siteAccess

However if I type by hand the url: http://www.domain.com/en/my-link, the link is correct, I'm not redirected.
As a result, I'm on an URL where the default siteAccess is included, it's not removed as asked by RemoveSiteAccessIfDefaultAccess=enabled

index.php should perform a redirect to the url:
http://www.domain.com/my-link

For now, I've added a crappy patch in my index.php to correct this bad behavior, waiting for a better solution...

at around line 340, after the code:

$access = eZSiteAccess::match( $uri,
                      eZSys::hostname(),
                      eZSys::serverPort(),
                      eZSys::indexFile() );
$access = eZSiteAccess::change( $access );
eZDebugSetting::writeDebug( 'kernel-siteaccess', $access, 'current siteaccess' );

I've added the code:

if ( $ini->variable( 'SiteAccessSettings', 'RemoveSiteAccessIfDefaultAccess' ) == "enabled" &&
     $access["name"] == $ini->variable( 'SiteSettings', 'DefaultAccess' ) &&
     !empty($access["uri_part"]) )
{
    $redir = $uri->attribute("original_uri");
    eZURI::transformURI($redir);
    eZHTTPTool::redirect($redir);
    eZExecution::cleanExit();
}