I think it is definitely related to the cheevos. When I load up RetroArch from the RetroPie menu, the controller is detected instantly like always. When I try to load a game, it takes a long time before detecting. When I disable the cheevos and load up the same game, the controller is recognized instantly too. The strange thing is, it waits like it's connecting to the server, but doesn't pop up my profile being logged in until AFTER it detects my controller. Even then, it's slow popping up the list of earned cheevos for me. I wonder if there's work being done on that side of the system?
@meleu - Anything going on you know of?