ok, tried the autoflush, and it looked like it was working, but then,,...it started again, a "done" message in the status bar and blank screen, except for a incrementing "ticker" to indicate progress that was now autoflushing. This time the process lasted 50 seconds. Do you think procmon would kill the process? and if so, shouldnt this return the user some http error such as 500 ? I checked my log the time that the latest failure occured, and the script had just stopped. No die signal was received, it just stopped.
Are you also writing output periodically? Take a look at the spelled sub in the Jumble solver script. It periodically prints out ".oOo.oOo" string to the browser. Are you doing something like that? If not you'll timeout even though you set autoflush.