Mark,
Stranger things have happened and it is tough to troubleshoot from here. I'd suggest putting in some kind of debug routine to narrow down exactly where the problem is occurring. For example, in this case I would probably have my script select each paragraph as it walks through the source file, then pop up a confirm() box which aborts the script on No. That way, you can find out exactly where the script gets lost. At first, maybe have it stop every 10 paragraphs or so, since you have such a large file. It's a bit time consuming, but often it's what you have to do in this environment. You might be surprised what you find and it is possible that the file length is a red herring.
Russ