If you change the config to FCKConfig.EMailProtection = 'none' ;
you should get the old behaviour (and I think that it should be the default, because those encrypted links aren't usable by people with javascript disabled.
to fix the IE error, it seems that changing from <a href="javascript:location.href='mailto:'+String.fromCharCode(109,97,105,108,64,101,120,97,109,112,108,101,46,99,111,109)+'?'">
to <a href="javascript:void(location.href='mailto:'+String.fromCharCode(109,97,105,108,64,101,120,97,109,112,108,101,46,99,111,109)+'?')">
is enough