1. I experienced this for the first time after creating a set of 4 groups. (I was already member of 49 messaging enabled groups divided in two courses).

2. This took the Group Message list count to 53, but two of the four created groups were not showing in the list.

3. I took myself out of some of the other 49 groups, and, whenever I took myself out of an older group, one of the new groups appeared in the messaging list.

4. The issue persists, if I create a new group with enabled messaging and join it, It will not show up in my Group messages list, until I remove myself from another group. 

The fact that it is fixed "one at a time" (remove myself from one group, one of the new shows up) and the persistence in the behaviour makes me  think there's a hard, hidden, limit in the number of groups showing up in the message list, rather than that I was facing some db update issue.