These are really, really tough to troubleshoot. Basically, you'll want to just start excluding file and registry data until it builds the *.ism successfully.
Like a CS professor of mine once said, "Divide and Conquer". Start by excluding half of all data. Then when you find the half that lets you build successfully, exclude everything but one half of that subset, and so on...
It takes a while, but eventually you end up with the culprit. I'll see if I can do some searching through old files and find the source of this problem the last time I had encountered it....