I recentrly got a Yamaha A3000 from Ebay and started fiddling with a Gotek I had around, where FlashFloppy was already installed.
After a bit of trial and error, and looking online, the correct way to have the Gotek installed is to set the jumpers BOTH on S1 and JC.
I had to reset the Gotek first (press and hold both buttons for 3secs, with no pendrve in it) so it is "standard" settings, with no FF.CFG installed.