I know you posted a long time ago (I don't know if you're still around - I saw that your last visit was on march 13, 2016). However, if you ever see this post, here is the solution: in the Launchbox go to Edit Game -> Emulation -> Edit -> in "Command Line Standard Parameter", insert the code "-n -fs 1" .
Just restored the scripts to handle the 2 binaries + the dlls for versions >= 0.90, it's mainly for the old versions page, but the latest page (main download page) is handled by them now again.
Next time : the linux binary, oh yeah... (well maybe then, but no hurry !).