We were also having this issue with our site. After updating to the 0.5.5 and checking "Redirect administration pages to site's original domain (remote login disabled if this redirect is disabled)" I am noticing that when trying to access the wp-login.php on subsites it doesn't redirect to the subdomain url for logging in. It stays on a page similar to what "helpology" mentioned.
We fixed the issue but using 0.5.4.3 in which we have "Redirect administration pages to site's original domain (remote login disabled if this redirect is disabled)" checked and also "Remote Login" checked. If we do not check "Remote Login" then when trying to go to the login screen for a subsite it doesn't redirect to the subdomain login. If I try to login on the mapped domain then I am sent to a 404 which is my ip followed by a $ so something like "123.123.123.123/$".
Biggest thing that I noticed with 0.5.5 was that I was unable to login to subsites at all (including using super admin). I had to login to the root site and then go to the backend to access it.