The GoldenGate does not work correctly with an 68060 nor with OS3.9.
Try an 030 based Kick 3.1 machine, if you have one.
That is not correct mate since I used an GG 386 perfectly in my former A4000D 060/PPC+CVisionPPC with OS3.9+BB3 (at the time) so I can say that there was NO issue whatsoever. I also installed DOS 6.22+Windows 3.11+Office 4.3 Pro without any issue as well.
GG 486 can be picky though, since I tested in the same setup an GG486 and wasn't working at all (Early startup didn't see it as well).
The only thing I know for sure is that the GG's aren't working with a frequency larger than 50MHz (for 060's) since a close friend of mine tried 60MHz overclock (via new mask 060) and GG wasn't working at all. Upon changing the oscillator back to 50MHz GG was working again just fine.
GL