hey Will
this is an issue that has been brought up before on the board. I think (though I am not sure) that R's behavior with respect to readline changed at some point, but from what I can tell all the readline() commands have to be switched to scan(). As I mentioned somewhere before on the board, I have made 3dGC.R work in batch mode this way, but have not sent Gang a fix for 1dSVAR, partly because I really don't understand it as well as I should!
James