I remember other customers had problems with the Gotek emulator as well, and solved them by using a real floppy drive. We have neither tested, nor advertised it to work with a floppy emulator. Since this is an end-of-life product, this part will most likely not be changed.
We don't even have that floppy emulator for testing. To my knowledge, it's a hacked software, so it may be a good idea to turn to the person who made the Amiga-support of the Gotek emulators. Since the ACA500 works great with a real floppy drive, it's a clear indication that the floppy emulator is not entirely fit for the purpose of replacing a drive.