Hey nitram thanx for reply!
The executable is a CLI application, its not using X, its character based. There is no graphical window manager on (Micro)Core, so there are no "/home/tc/.X.d/startups", not needed for this.
BTW it's an embedded system without network connection, and limited keyboard interface, it doesn't matter if its root or not, as long as it has permission to write to the CF card...