I think it's 'workbench.library' that is missing in the A4000T ROM when compared to other Amiga models, hence they needed a unique Workbench disk with that library included (due to space constraints on the ROM). I'm not sure about Setpatch. However, a clean 3.9 install is highly likely to know about all of that I'm sure! Anyway, it loads Workbench so I sincerely doubt that is the issue here.
It's been a long time since I thoroughly read the MMULib docs, but I'm pretty sure I patched my Setpatch (via included patch) so that it loads the correct 680x0.library directly via hardware detection instead of this 68040.dummy library nonsense. You might want to read the docs to see if it can be loaded via the 68040 dummy library. I'm not sure off of the top of my head as it's been years since I used the dummy library. I know for sure I don't have a dummy library in my libs and haven't done for years and years. Thor does include an Install script for the whole package which he assures us takes care of everything. I've never used it, but he's usually right about things.
Of course, your other option of testing is custom boot disks. Make up a Workbench disk with the Quikpak libs installed and do a cold boot of the disk. Run some floppy based software. I wouldn't start running programs from your hard drives unless you know what you're doing regarding the 4GB limit in the 3.1 ROM etc. Also, It could be a reset resident module on your 3.9 install causing trouble. Have you made any changes recently on both machines which correlate with these errors you are seeing? Anything new been added to the startup-sequence or WBStartup etc?
