are you using LSX or LSX VOID ?
LSX likely doesnt work with IG3 i havent updated it in a while. IG3 did funky things with the keyboard shortcuts. But LSX VOID fully takes advantage of IG3, almost to the point of rape.
which .exe files are you curious about in LSTOOLS, they all do different things. Some of them are used directly by the skin, some of them are for integration with other applications.
But in either case, whenever LSX or LSXVOID want to call a script, this is where it calls them from.