Phil,

Useful info there and it sounds like you're making headway into solving this - if so it would be invaluable to add your findings to this thread as you go, for the next poor soul who buys these (I also have 5 of these lying around... definitely not TB6600s, despite the eBay ad claiming them to be so - I think there's a hint as to the max voltage printed on the enclosure - I think (I'm at work at the moment) that the TB6600-based ones advertise themselves at upto 48V operating, whereas your's (and mine) at 40V are the little SMD devices. I'll also caution that the opto-isolators on that board are (according to datasheet) pretty sluggish devices - but chase one problem at a time and see if your thermal solution resolves your problems.