i had issues with an Apollo board 1240 like you, same errors. Turns out i had the Happy New Year virus, which attaches itself to many C commands, including the 68040.library, and also many programs like DOpus and scala. It makes the infected files a few kb bigger. Eventually i had to reformat the hard drive and get system floppies from somewhere else because the ones I had were infected. I'd run VirusZ to make sure.
