o_dog: Testing shows another issue that will be of interest to scripters. It's starting to look like a script that runs longer than the idle timeout on a non-exempt user will end up returning a script failure message and be disconnected when the script finally finishes. This probably only matters for things like 'site rescan all' on a big directory since the default idle timeout of 6 minutes is pretty long for a script to be running. Idle exempt users won't trigger this which is probably why I never noticed it before
I've duplicated the result, but haven't confirmed the exact problem but thought I'd mention it so you can make sure you test your script with an idle exempt user since this wouldn't be a bug in your script that you need to find.