Wow, the more you reveal the more I wonder if you should even try to load a backed up version of your EPROM onto a new ECM for fear of transfering whatever glitch you have right over to the new ECM. Right now you dont really know if the issue lies with the hardware or software and thats a little scary.
Best case you have a hardware issue and you dump your current EPROM into a new ECM and every thing works perfectly.
Worse case you have to get a new ECM and start all over with tuning.. You should be able to manually enter the values from all your tables safely though...
In my line of work I've seen wierder ****. I had a 290,000 dollar robot pick up a virus from a 400 dollar lap top, the virus had zero impact on the lap top, but when it hit that robot control it was over.