Third party plugins are nothing to do with Launchbox or whether you have a license or not. We offer the plugin system, but that is it, none of the available plugins are vetted or maintained by the Launchbox devs, they are wholly maintained by the plugins author, it makes no difference if you payed for a license or not. Also you accepted this agreement when you downloaded any "Third Party" plugin or program.
This is likely due to the fact that the store launchers are launched, and then minimized, so that is the window being tracked. I'm not sure about Battle.net off hand, but steam has it's own built in playtime tracker anyway. At the end of the day these features are not officially supported by Launchbox, hence they can be a little wonky, they are added by users and are not our code, plugin creators can only work with the tools they have been given by us, if those tools dont cater to specific uses there is nothing the plugin creators can do about that.