With the 6.4.1.0 version of the SQL management pack the SQL 2012 DB Engine group does not contain all SQL 2012 servers. This is due to the group being populated based on a SQL registry key which is looking for a version value of 11.0.xxxx.x, however when updating SQL 2012 to SP1 the version changes to 11.1.xxx.x

Kevin Holman has written a nice blog entry about this particular issue: here. As well as an addendum management pack that contains a new group population discovery set to “11.*” along with an override to disable the built in group, which is available for download at the bottom of his article.