I have this kinda problem. I recently got amigaOS3.9 working on my 'A2000 (thanks Ryu) and I have one slight problem... well okay it's kinda big.
If I use the Setpatch it came with, with no extra settings, everything works fine, but my GFX card's software, RetinaEmu (no it can't use CGX) won't put the workbench on thru the Retina. If I replace that setpatch with an older one (like the one from Aminet, or the 3.1 disks) RetinaEmu works, but now none of the prefs work, and WBloader+ doesn't work. Does the new Setpatch do something that might interfere with the retina, what does it do differently from older setpatchs?