Recently I've been installing OS3.9 with BoingBags, I said yes to install ROM Updates. I wonder, are the ROM updates just installed onto the CF and then mapped to memory or do they actually write over my physical Amiga ROM?? Could this be the problem??
ROM (Read Only Memory) can *not* be written.
The AmigaOS 3.9 ROM update is installed to "DEVS:AmigaOS ROM Update". It will not be used if you rename or delete it. It's installed by a new for AmigaOS 3.9 C:SetPatch (version 44.38) which is executed at the beginning of S:Startup-Sequence. It can be skipped. My SetPatch line is "SetPatch NOROMUPDATE QUIET". I disable the MAPROM and use BlizKick to put a custom kickstart in MAPROM.
The only other things I've done is set up networks between my Amiga and PC. But when I found out those games weren't working I reverted back to an absolutely clean install of ClassicWB with original 3.1 WB disks, but still I am having these problems.
WHDLoad may not work with networking enabled (interrupts don't work right) but I don't think that is your problem judging by the error message.