I wasn't sure what the LSDJBuilder.exe was for, and it seems to only take a patched file...question is which one?!
What I get when adding the LSDJ rom in the menu builder is that it's 32k, where I was expecting something larger. I know that when I used the dumps of the banks from before (when there were 3 LSDJs with full save capabilities) it shows up as 256 etc. as you say, so I kind of knew that it wasn't going to work, but had a go anyway.
Thanks for your help. When I get this sorted I'll write a readme.txt/blog post on how to patch lsdj and get it working so that someone can learn from my pain! Kind of surprised that that hasn't been done already though....