Aloha!
I think I ran into this regression with v1.16 beta4 and filed a ticket.
So far I have seen this to affect indexes, primary keys and foreign keys
But *not* tables, views, function, triggers, sequences or types ...
Added two small screenshots to the ticket to compare 1.4 and 1.16b4
http://code.pgadmin.org/trac/ticket/377
Regards
Erwin