I was just wondering if you had any FPU optimized libraries in your libs: directory rather than the stock OS ones. Of course the 'EC060 would puke on those as well. I used to use the program PowerPacker and it needed a library to operate. When I booted up my floppy on a non-020/881 based machine - things started failing left and right. I was wondering if you might be encountering the same sort of issue. I would take all of your existing libraries aside, replace them with bog-standard OS ones (save the special '060 and '040 replacement ones) and try again.
Just my 2 cents...