Are you sure that your USBLGX is the latest version as I was having this problem and as soon as I updated all my nintendont settings in USBLGX worked fine. Also autoboot enabled should make nintendont load the chosen game automatically without having to select it again in nintendont.
I'm pretty certain it is the latest version. Unless the built-in updater no longer works?
EDIT: Double-checked. I am running the latest version available through the USBLGX built-in updater, "Built Jan 20 2015" Rev1233. Nintendont autoboot is enabled in USBLGX's settings. I'm still getting the prompt to choose between USB and SD and to pick a game when loading a game from USBLGX as the front end.