I have posted a preliminary version of my discussion about the bootloading process
here. I'll try to tidy it up a little over the next few days and add more troubleshooting hints when I think of them.
It goes into more detail than any sane person could want to know about booting Altairs, I hope it's not to dull to read.
Unfortunately, I can't do any more testing with windows for a while. My file server went down hard today and I had to scavenge my windows machine to get it running again. I'll do more testing when I get a new motherboard for it.