Have you tried to a remote debug of the executable to see where it is hanging?
Or add features to the program that logs things to a file or show strings in a string indicator so you can see how far the VI has progressed at the time it is hung.
I did the remote debug and found that it was hanging on a file close operation. So I did some research and found that the write characters to file vi I was using was removed and so I switch all of those and now it seems to be working pretty well.
