The Navigation Manager continues to be a major failing for me in the TDP 18.104.22.16874 beta. It cannot seem to remember much of anything when switching connections from one database server to another (Oracle 11gR1 to SQL Server 2008 R2 and back in my case).
I work with multiple database servers and databases and when switching connections I expect Toad to revert back to the connection environment state of when that connection was last used. The latest version still working for me generally in this regard is TDP 22.214.171.1246, which can also handle multiple connections to the same database server (looking at different schemas or databases).
I suggest the developers handling the Navigation Manager back up and regroup because they seem to have lost their way.