I noticed that games giving this issue had launch arguments appended to them in Launchbox (Edit game -> Emulation tab) that didn't quite match up with what was in my pcsx2\inis\ folder.
I've downloaded the database of games from the repo and put them in my LaunchBox\Plugins\PCSX2Configuator\Game Configs\ folder.
I wiped all my games out in Launchbox and readded them and I'm not having the launching issue now, but how do I know if they're truly accepting the preset game configs? After launching a game, my "Use Custom Command-Line Parameters" for that respective game in Launchbox is empty and not pointing to anything, this means the plugin is not working, correct? The game in question does have a folder inside of \Game Configs\.
Perhaps I should delete my entire \Game Configs\ folder and let the plugin manually download everything by attempting to launch each game and test it that way? Is there any other way to know if the plugin is working?