I am running WP 3.3 and Mapping plugin Version 0.5.4.2
I think this is a WP 3.3/Plugin issue. Here is what you can do to re-produce.
Setup two sites with the same user.
Log into one of them directly with mapping enabled, you get the URL of that site for example http://www.domain2.com/wp-admin is fine.
However try and switch under "My Sites" to site3 and you are FIRST redirected to http://www.domain.com/wp-login (Main site URL), and once you login there you are then brought to http://www.domain3.com/wp-login.
You are thus required to authenticate twice to move between "my sites". It seems something is not being mapped or re-directed properly in 3.3 for the "my sites" links. I have only the standard .htaccess file per the multi-site setup, nothing different.
Once you are authenticated you can move between the two and the URL is correctly shown. Only on the first jump are you given the MAIN site url THEN the correct site URL. Definitely seems to be a bug. Can anyone else confirm? It is essentially like it wants you to authenticate to the Main site first which makes no sense.