The input file attached works without the last subgraph. It seems like at some point the nodes get over constrained or something.
In any case I get a windows crash screen. Microsoft offers to send in a report, which says that dot.exe crashed. There is a file with a dump of the driver state. I can post it if anyone is interested.
I tried removing all labels on edges and that didn't help.
I am not using the command window to run graphviz and
I can't see how to get the version.
Input file: b1136.dot