There is another thread here
https://forum.amiga.org/index.php?topic=5463.0 that descibes my problem exactly. I got OS 2.9 running and then did an install of AmiFTP. It worked fine - until I rebooted. Now I get messages like:
Cannot open "resource.library", version 44
when I try to run AmiDock (although I do have that file in LIBS:) and
Can't open version 40 of gadgets/fuelgauge.gadget
when I try to run AmiFTP.(and I have that file too).
Unfortunately, even after reading that thread I still don't understand how to fix this. One suggestion was toi replace C:SetPatch from the 3.9 CD, but my CD has no SetPatch in its C directory. I did replace it from my USB backup but I think that was the same file (it was the same size anyway, 31.8K) and that didn't fix the problem anyway. Another post suggests that some classes are missing somewhere but I can't tell which ones.
And a number of other programs won't start now either. Could someone please help me out of this mess? I'm totally stumped here.
FWIW, I'm using KS 40.63, WB 45.1 and SetPatch 44.13
FWIW2: If I boot from the Emergency 3.9 Rescue Disk, AmiDock works OK but my primary boot disk FS3: does not appear on the WB screen.