This is a bit strange -- the Select Connection dialog should appear, but the Choose a Connection dialog is unexpected. That dialog is present in the code base, but it is not clear how it is getting triggered, and I cannot even recall what context I might have seen it in, if ever. All the connections are picked from the Select Connection dialog or the ConnectionSelectorUI's list of values. Perhaps it is "dead code" that is getting called due to some corruption in the user settings.
If you are not already on 4.0.3, you might try installing that, then skip the step for migrating user settings. Otherwise try restarting SQL Developer after renaming the systemN.N.N.NN.NN directory for your current release.
SQL Developer Team